Starting phenix.real_space_refine on Wed Apr 10 22:09:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sev_40430/04_2024/8sev_40430_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sev_40430/04_2024/8sev_40430.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sev_40430/04_2024/8sev_40430.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sev_40430/04_2024/8sev_40430.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sev_40430/04_2024/8sev_40430_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sev_40430/04_2024/8sev_40430_updated.pdb" } resolution = 3.17 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= 0.123 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 12 5.49 5 S 164 5.16 5 C 13380 2.51 5 N 3284 2.21 5 O 3788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 3962": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 3968": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 4018": "OD1" <-> "OD2" Residue "A GLU 4056": "OE1" <-> "OE2" Residue "A GLU 4199": "OE1" <-> "OE2" Residue "A GLU 4206": "OE1" <-> "OE2" Residue "A PHE 4219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 4220": "OD1" <-> "OD2" Residue "A GLU 4227": "OE1" <-> "OE2" Residue "A GLU 4244": "OE1" <-> "OE2" Residue "A PHE 4579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4676": "OE1" <-> "OE2" Residue "A PHE 4732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4856": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 4868": "OD1" <-> "OD2" Residue "A GLU 4871": "OE1" <-> "OE2" Residue "A ASP 4966": "OD1" <-> "OD2" Residue "A GLU 4981": "OE1" <-> "OE2" Residue "A ASP 5020": "OD1" <-> "OD2" Residue "B PHE 3962": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 3968": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 4018": "OD1" <-> "OD2" Residue "B GLU 4056": "OE1" <-> "OE2" Residue "B GLU 4199": "OE1" <-> "OE2" Residue "B GLU 4206": "OE1" <-> "OE2" Residue "B PHE 4219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 4220": "OD1" <-> "OD2" Residue "B GLU 4227": "OE1" <-> "OE2" Residue "B GLU 4244": "OE1" <-> "OE2" Residue "B PHE 4579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4676": "OE1" <-> "OE2" Residue "B PHE 4732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4856": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 4868": "OD1" <-> "OD2" Residue "B GLU 4871": "OE1" <-> "OE2" Residue "B ASP 4966": "OD1" <-> "OD2" Residue "B GLU 4981": "OE1" <-> "OE2" Residue "B ASP 5020": "OD1" <-> "OD2" Residue "C PHE 3962": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 3968": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 4018": "OD1" <-> "OD2" Residue "C GLU 4056": "OE1" <-> "OE2" Residue "C GLU 4199": "OE1" <-> "OE2" Residue "C GLU 4206": "OE1" <-> "OE2" Residue "C PHE 4219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 4220": "OD1" <-> "OD2" Residue "C GLU 4227": "OE1" <-> "OE2" Residue "C GLU 4244": "OE1" <-> "OE2" Residue "C PHE 4579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4676": "OE1" <-> "OE2" Residue "C PHE 4732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4856": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 4868": "OD1" <-> "OD2" Residue "C GLU 4871": "OE1" <-> "OE2" Residue "C ASP 4966": "OD1" <-> "OD2" Residue "C GLU 4981": "OE1" <-> "OE2" Residue "C ASP 5020": "OD1" <-> "OD2" Residue "D PHE 3962": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 3968": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 4018": "OD1" <-> "OD2" Residue "D GLU 4056": "OE1" <-> "OE2" Residue "D GLU 4199": "OE1" <-> "OE2" Residue "D GLU 4206": "OE1" <-> "OE2" Residue "D PHE 4219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 4220": "OD1" <-> "OD2" Residue "D GLU 4227": "OE1" <-> "OE2" Residue "D GLU 4244": "OE1" <-> "OE2" Residue "D PHE 4579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4676": "OE1" <-> "OE2" Residue "D PHE 4732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4856": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 4868": "OD1" <-> "OD2" Residue "D GLU 4871": "OE1" <-> "OE2" Residue "D ASP 4966": "OD1" <-> "OD2" Residue "D GLU 4981": "OE1" <-> "OE2" Residue "D ASP 5020": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 20632 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5126 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 15, 'TRANS': 610} Chain breaks: 4 Chain: "B" Number of atoms: 5126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5126 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 15, 'TRANS': 610} Chain breaks: 4 Chain: "C" Number of atoms: 5126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5126 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 15, 'TRANS': 610} Chain breaks: 4 Chain: "D" Number of atoms: 5126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5126 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 15, 'TRANS': 610} Chain breaks: 4 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4452 SG CYS A4958 57.043 82.993 88.700 1.00 62.76 S ATOM 4477 SG CYS A4961 59.631 83.670 91.460 1.00 61.89 S ATOM 9578 SG CYS B4958 61.263 57.043 88.700 1.00 63.22 S ATOM 9603 SG CYS B4961 60.585 59.630 91.460 1.00 62.33 S ATOM 14704 SG CYS C4958 87.213 61.263 88.700 1.00 64.07 S ATOM 14729 SG CYS C4961 84.625 60.585 91.459 1.00 63.16 S ATOM 19830 SG CYS D4958 82.993 87.213 88.700 1.00 64.33 S ATOM 19855 SG CYS D4961 83.670 84.625 91.460 1.00 63.21 S Time building chain proxies: 10.67, per 1000 atoms: 0.52 Number of scatterers: 20632 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 164 16.00 P 12 15.00 O 3788 8.00 N 3284 7.00 C 13380 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A4876 " - pdb=" SG CYS A4882 " distance=2.03 Simple disulfide: pdb=" SG CYS B4876 " - pdb=" SG CYS B4882 " distance=2.03 Simple disulfide: pdb=" SG CYS C4876 " - pdb=" SG CYS C4882 " distance=2.03 Simple disulfide: pdb=" SG CYS D4876 " - pdb=" SG CYS D4882 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.73 Conformation dependent library (CDL) restraints added in 3.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5102 " pdb="ZN ZN A5102 " - pdb=" ND1 HIS A4983 " pdb="ZN ZN A5102 " - pdb=" NE2 HIS A4978 " pdb="ZN ZN A5102 " - pdb=" SG CYS A4958 " pdb="ZN ZN A5102 " - pdb=" SG CYS A4961 " pdb=" ZN B5102 " pdb="ZN ZN B5102 " - pdb=" ND1 HIS B4983 " pdb="ZN ZN B5102 " - pdb=" NE2 HIS B4978 " pdb="ZN ZN B5102 " - pdb=" SG CYS B4961 " pdb="ZN ZN B5102 " - pdb=" SG CYS B4958 " pdb=" ZN C5102 " pdb="ZN ZN C5102 " - pdb=" ND1 HIS C4983 " pdb="ZN ZN C5102 " - pdb=" NE2 HIS C4978 " pdb="ZN ZN C5102 " - pdb=" SG CYS C4961 " pdb="ZN ZN C5102 " - pdb=" SG CYS C4958 " pdb=" ZN D5102 " pdb="ZN ZN D5102 " - pdb=" ND1 HIS D4983 " pdb="ZN ZN D5102 " - pdb=" NE2 HIS D4978 " pdb="ZN ZN D5102 " - pdb=" SG CYS D4961 " pdb="ZN ZN D5102 " - pdb=" SG CYS D4958 " Number of angles added : 8 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4712 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 128 helices and 8 sheets defined 70.4% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.21 Creating SS restraints... Processing helix chain 'A' and resid 3951 through 3969 removed outlier: 3.513A 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 3989 Processing helix chain 'A' and resid 3993 through 4005 removed outlier: 4.051A pdb=" N MET A4000 " --> pdb=" O PHE A3996 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLN A4005 " --> pdb=" O MET A4001 " (cutoff:3.500A) Processing helix chain 'A' and resid 4007 through 4030 removed outlier: 3.981A pdb=" N ILE A4010 " --> pdb=" O SER A4007 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N GLU A4011 " --> pdb=" O SER A4008 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP A4018 " --> pdb=" O GLU A4015 " (cutoff:3.500A) Processing helix chain 'A' and resid 4039 through 4050 removed outlier: 3.634A pdb=" N VAL A4045 " --> pdb=" O ALA A4041 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP A4046 " --> pdb=" O ARG A4042 " (cutoff:3.500A) Processing helix chain 'A' and resid 4052 through 4059 Processing helix chain 'A' and resid 4199 through 4205 Processing helix chain 'A' and resid 4208 through 4223 Processing helix chain 'A' and resid 4230 through 4251 Processing helix chain 'A' and resid 4541 through 4557 removed outlier: 3.771A pdb=" N VAL A4546 " --> pdb=" O GLY A4542 " (cutoff:3.500A) Processing helix chain 'A' and resid 4559 through 4579 removed outlier: 4.151A pdb=" N PHE A4579 " --> pdb=" O PHE A4575 " (cutoff:3.500A) Processing helix chain 'A' and resid 4639 through 4664 removed outlier: 3.572A pdb=" N LEU A4652 " --> pdb=" O LEU A4648 " (cutoff:3.500A) Processing helix chain 'A' and resid 4666 through 4683 Processing helix chain 'A' and resid 4697 through 4705 removed outlier: 4.477A pdb=" N LEU A4704 " --> pdb=" O GLN A4700 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N VAL A4705 " --> pdb=" O TRP A4701 " (cutoff:3.500A) Processing helix chain 'A' and resid 4718 through 4732 removed outlier: 4.364A pdb=" N LYS A4721 " --> pdb=" O LYS A4718 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N GLY A4729 " --> pdb=" O ASP A4726 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ASP A4730 " --> pdb=" O LYS A4727 " (cutoff:3.500A) Processing helix chain 'A' and resid 4735 through 4741 Processing helix chain 'A' and resid 4773 through 4785 Processing helix chain 'A' and resid 4787 through 4804 removed outlier: 3.975A pdb=" N HIS A4803 " --> pdb=" O SER A4799 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TYR A4804 " --> pdb=" O LEU A4800 " (cutoff:3.500A) Processing helix chain 'A' and resid 4806 through 4819 Processing helix chain 'A' and resid 4821 through 4858 removed outlier: 3.806A pdb=" N SER A4829 " --> pdb=" O THR A4825 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL A4830 " --> pdb=" O ILE A4826 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASN A4833 " --> pdb=" O SER A4829 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY A4834 " --> pdb=" O VAL A4830 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LYS A4835 " --> pdb=" O THR A4831 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLN A4836 " --> pdb=" O HIS A4832 " (cutoff:3.500A) Processing helix chain 'A' and resid 4869 through 4871 No H-bonds generated for 'chain 'A' and resid 4869 through 4871' Processing helix chain 'A' and resid 4879 through 4892 removed outlier: 4.334A pdb=" N VAL A4891 " --> pdb=" O MET A4887 " (cutoff:3.500A) Processing helix chain 'A' and resid 4910 through 4924 removed outlier: 3.587A pdb=" N VAL A4915 " --> pdb=" O LEU A4911 " (cutoff:3.500A) Processing helix chain 'A' and resid 4927 through 4956 removed outlier: 4.586A pdb=" N ILE A4932 " --> pdb=" O LEU A4928 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN A4933 " --> pdb=" O LEU A4929 " (cutoff:3.500A) Processing helix chain 'A' and resid 4965 through 4970 removed outlier: 4.270A pdb=" N THR A4970 " --> pdb=" O ASP A4966 " (cutoff:3.500A) Processing helix chain 'A' and resid 4974 through 4981 Processing helix chain 'A' and resid 4985 through 4997 Processing helix chain 'A' and resid 5000 through 5002 No H-bonds generated for 'chain 'A' and resid 5000 through 5002' Processing helix chain 'A' and resid 5005 through 5015 Processing helix chain 'A' and resid 5028 through 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: 3.513A 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 3989 Processing helix chain 'B' and resid 3993 through 4005 removed outlier: 4.051A pdb=" N MET B4000 " --> pdb=" O PHE B3996 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLN B4005 " --> pdb=" O MET B4001 " (cutoff:3.500A) Processing helix chain 'B' and resid 4007 through 4030 removed outlier: 3.981A pdb=" N ILE B4010 " --> pdb=" O SER B4007 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N GLU B4011 " --> pdb=" O SER B4008 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP B4018 " --> pdb=" O GLU B4015 " (cutoff:3.500A) Processing helix chain 'B' and resid 4039 through 4050 removed outlier: 3.634A pdb=" N VAL B4045 " --> pdb=" O ALA B4041 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP B4046 " --> pdb=" O ARG B4042 " (cutoff:3.500A) Processing helix chain 'B' and resid 4052 through 4059 Processing helix chain 'B' and resid 4199 through 4205 Processing helix chain 'B' and resid 4208 through 4223 Processing helix chain 'B' and resid 4230 through 4251 Processing helix chain 'B' and resid 4541 through 4557 removed outlier: 3.771A pdb=" N VAL B4546 " --> pdb=" O GLY B4542 " (cutoff:3.500A) Processing helix chain 'B' and resid 4559 through 4579 removed outlier: 4.152A pdb=" N PHE B4579 " --> pdb=" O PHE B4575 " (cutoff:3.500A) Processing helix chain 'B' and resid 4639 through 4664 removed outlier: 3.572A pdb=" N LEU B4652 " --> pdb=" O LEU B4648 " (cutoff:3.500A) Processing helix chain 'B' and resid 4666 through 4683 Processing helix chain 'B' and resid 4697 through 4705 removed outlier: 4.477A pdb=" N LEU B4704 " --> pdb=" O GLN B4700 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N VAL B4705 " --> pdb=" O TRP B4701 " (cutoff:3.500A) Processing helix chain 'B' and resid 4718 through 4732 removed outlier: 4.364A pdb=" N LYS B4721 " --> pdb=" O LYS B4718 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N GLY B4729 " --> pdb=" O ASP B4726 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ASP B4730 " --> pdb=" O LYS B4727 " (cutoff:3.500A) Processing helix chain 'B' and resid 4735 through 4741 Processing helix chain 'B' and resid 4773 through 4785 Processing helix chain 'B' and resid 4787 through 4804 removed outlier: 3.974A pdb=" N HIS B4803 " --> pdb=" O SER B4799 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TYR B4804 " --> pdb=" O LEU B4800 " (cutoff:3.500A) Processing helix chain 'B' and resid 4806 through 4819 Processing helix chain 'B' and resid 4821 through 4858 removed outlier: 3.769A pdb=" N SER B4829 " --> pdb=" O THR B4825 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL B4830 " --> pdb=" O ILE B4826 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ASN B4833 " --> pdb=" O SER B4829 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY B4834 " --> pdb=" O VAL B4830 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LYS B4835 " --> pdb=" O THR B4831 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLN B4836 " --> pdb=" O HIS B4832 " (cutoff:3.500A) Processing helix chain 'B' and resid 4869 through 4871 No H-bonds generated for 'chain 'B' and resid 4869 through 4871' Processing helix chain 'B' and resid 4879 through 4892 removed outlier: 4.334A pdb=" N VAL B4891 " --> pdb=" O MET B4887 " (cutoff:3.500A) Processing helix chain 'B' and resid 4910 through 4924 removed outlier: 3.587A pdb=" N VAL B4915 " --> pdb=" O LEU B4911 " (cutoff:3.500A) Processing helix chain 'B' and resid 4927 through 4956 removed outlier: 4.586A pdb=" N ILE B4932 " --> pdb=" O LEU B4928 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN B4933 " --> pdb=" O LEU B4929 " (cutoff:3.500A) Processing helix chain 'B' and resid 4965 through 4970 removed outlier: 4.270A pdb=" N THR B4970 " --> pdb=" O ASP B4966 " (cutoff:3.500A) Processing helix chain 'B' and resid 4974 through 4981 Processing helix chain 'B' and resid 4985 through 4997 Processing helix chain 'B' and resid 5000 through 5002 No H-bonds generated for 'chain 'B' and resid 5000 through 5002' Processing helix chain 'B' and resid 5005 through 5015 Processing helix chain 'B' and resid 5028 through 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 Processing helix chain 'C' and resid 3974 through 3981 Processing helix chain 'C' and resid 3985 through 3989 Processing helix chain 'C' and resid 3993 through 4005 removed outlier: 4.012A pdb=" N MET C4000 " --> pdb=" O PHE C3996 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN C4005 " --> pdb=" O MET C4001 " (cutoff:3.500A) Processing helix chain 'C' and resid 4007 through 4030 removed outlier: 3.982A pdb=" N ILE C4010 " --> pdb=" O SER C4007 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N GLU C4011 " --> pdb=" O SER C4008 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP C4018 " --> pdb=" O GLU C4015 " (cutoff:3.500A) Processing helix chain 'C' and resid 4039 through 4050 removed outlier: 3.509A pdb=" N VAL C4045 " --> pdb=" O ALA C4041 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP C4046 " --> pdb=" O ARG C4042 " (cutoff:3.500A) Processing helix chain 'C' and resid 4052 through 4059 Processing helix chain 'C' and resid 4199 through 4205 Processing helix chain 'C' and resid 4208 through 4223 Processing helix chain 'C' and resid 4230 through 4251 Processing helix chain 'C' and resid 4541 through 4557 removed outlier: 3.771A pdb=" N VAL C4546 " --> pdb=" O GLY C4542 " (cutoff:3.500A) Processing helix chain 'C' and resid 4559 through 4579 removed outlier: 4.151A pdb=" N PHE C4579 " --> pdb=" O PHE C4575 " (cutoff:3.500A) Processing helix chain 'C' and resid 4639 through 4664 removed outlier: 3.571A pdb=" N LEU C4652 " --> pdb=" O LEU C4648 " (cutoff:3.500A) Processing helix chain 'C' and resid 4666 through 4683 Processing helix chain 'C' and resid 4697 through 4705 removed outlier: 4.477A pdb=" N LEU C4704 " --> pdb=" O GLN C4700 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N VAL C4705 " --> pdb=" O TRP C4701 " (cutoff:3.500A) Processing helix chain 'C' and resid 4718 through 4732 removed outlier: 4.364A pdb=" N LYS C4721 " --> pdb=" O LYS C4718 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N GLY C4729 " --> pdb=" O ASP C4726 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ASP C4730 " --> pdb=" O LYS C4727 " (cutoff:3.500A) Processing helix chain 'C' and resid 4735 through 4741 Processing helix chain 'C' and resid 4773 through 4785 Processing helix chain 'C' and resid 4787 through 4804 removed outlier: 3.971A pdb=" N HIS C4803 " --> pdb=" O SER C4799 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N TYR C4804 " --> pdb=" O LEU C4800 " (cutoff:3.500A) Processing helix chain 'C' and resid 4806 through 4819 Processing helix chain 'C' and resid 4821 through 4858 removed outlier: 3.768A pdb=" N SER C4829 " --> pdb=" O THR C4825 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL C4830 " --> pdb=" O ILE C4826 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASN C4833 " --> pdb=" O SER C4829 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY C4834 " --> pdb=" O VAL C4830 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LYS C4835 " --> pdb=" O THR C4831 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLN C4836 " --> pdb=" O HIS C4832 " (cutoff:3.500A) Processing helix chain 'C' and resid 4869 through 4871 No H-bonds generated for 'chain 'C' and resid 4869 through 4871' Processing helix chain 'C' and resid 4879 through 4892 removed outlier: 4.334A pdb=" N VAL C4891 " --> pdb=" O MET C4887 " (cutoff:3.500A) Processing helix chain 'C' and resid 4910 through 4924 removed outlier: 3.587A pdb=" N VAL C4915 " --> pdb=" O LEU C4911 " (cutoff:3.500A) Processing helix chain 'C' and resid 4927 through 4956 removed outlier: 4.586A pdb=" N ILE C4932 " --> pdb=" O LEU C4928 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN C4933 " --> pdb=" O LEU C4929 " (cutoff:3.500A) Processing helix chain 'C' and resid 4965 through 4970 removed outlier: 4.269A pdb=" N THR C4970 " --> pdb=" O ASP C4966 " (cutoff:3.500A) Processing helix chain 'C' and resid 4974 through 4981 Processing helix chain 'C' and resid 4985 through 4997 Processing helix chain 'C' and resid 5000 through 5002 No H-bonds generated for 'chain 'C' and resid 5000 through 5002' Processing helix chain 'C' and resid 5005 through 5015 Processing helix chain 'C' and resid 5028 through 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 Processing helix chain 'D' and resid 3974 through 3981 Processing helix chain 'D' and resid 3985 through 3989 Processing helix chain 'D' and resid 3993 through 4005 removed outlier: 4.012A pdb=" N MET D4000 " --> pdb=" O PHE D3996 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN D4005 " --> pdb=" O MET D4001 " (cutoff:3.500A) Processing helix chain 'D' and resid 4007 through 4030 removed outlier: 3.982A pdb=" N ILE D4010 " --> pdb=" O SER D4007 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N GLU D4011 " --> pdb=" O SER D4008 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP D4018 " --> pdb=" O GLU D4015 " (cutoff:3.500A) Processing helix chain 'D' and resid 4039 through 4050 removed outlier: 3.509A pdb=" N VAL D4045 " --> pdb=" O ALA D4041 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP D4046 " --> pdb=" O ARG D4042 " (cutoff:3.500A) Processing helix chain 'D' and resid 4052 through 4059 Processing helix chain 'D' and resid 4199 through 4205 Processing helix chain 'D' and resid 4208 through 4223 Processing helix chain 'D' and resid 4230 through 4251 Processing helix chain 'D' and resid 4541 through 4557 removed outlier: 3.771A pdb=" N VAL D4546 " --> pdb=" O GLY D4542 " (cutoff:3.500A) Processing helix chain 'D' and resid 4559 through 4579 removed outlier: 4.151A pdb=" N PHE D4579 " --> pdb=" O PHE D4575 " (cutoff:3.500A) Processing helix chain 'D' and resid 4639 through 4664 removed outlier: 3.572A pdb=" N LEU D4652 " --> pdb=" O LEU D4648 " (cutoff:3.500A) Processing helix chain 'D' and resid 4666 through 4683 Processing helix chain 'D' and resid 4697 through 4705 removed outlier: 4.477A pdb=" N LEU D4704 " --> pdb=" O GLN D4700 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N VAL D4705 " --> pdb=" O TRP D4701 " (cutoff:3.500A) Processing helix chain 'D' and resid 4718 through 4732 removed outlier: 4.364A pdb=" N LYS D4721 " --> pdb=" O LYS D4718 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N GLY D4729 " --> pdb=" O ASP D4726 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ASP D4730 " --> pdb=" O LYS D4727 " (cutoff:3.500A) Processing helix chain 'D' and resid 4735 through 4741 Processing helix chain 'D' and resid 4773 through 4785 Processing helix chain 'D' and resid 4787 through 4804 removed outlier: 3.974A pdb=" N HIS D4803 " --> pdb=" O SER D4799 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TYR D4804 " --> pdb=" O LEU D4800 " (cutoff:3.500A) Processing helix chain 'D' and resid 4806 through 4819 Processing helix chain 'D' and resid 4821 through 4858 removed outlier: 3.768A pdb=" N SER D4829 " --> pdb=" O THR D4825 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL D4830 " --> pdb=" O ILE D4826 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ASN D4833 " --> pdb=" O SER D4829 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY D4834 " --> pdb=" O VAL D4830 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N LYS D4835 " --> pdb=" O THR D4831 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLN D4836 " --> pdb=" O HIS D4832 " (cutoff:3.500A) Processing helix chain 'D' and resid 4869 through 4871 No H-bonds generated for 'chain 'D' and resid 4869 through 4871' Processing helix chain 'D' and resid 4879 through 4892 removed outlier: 4.334A pdb=" N VAL D4891 " --> pdb=" O MET D4887 " (cutoff:3.500A) Processing helix chain 'D' and resid 4910 through 4924 removed outlier: 3.587A pdb=" N VAL D4915 " --> pdb=" O LEU D4911 " (cutoff:3.500A) Processing helix chain 'D' and resid 4927 through 4956 removed outlier: 4.586A pdb=" N ILE D4932 " --> pdb=" O LEU D4928 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN D4933 " --> pdb=" O LEU D4929 " (cutoff:3.500A) Processing helix chain 'D' and resid 4965 through 4970 removed outlier: 4.269A pdb=" N THR D4970 " --> pdb=" O ASP D4966 " (cutoff:3.500A) Processing helix chain 'D' and resid 4974 through 4981 Processing helix chain 'D' and resid 4985 through 4997 Processing helix chain 'D' and resid 5000 through 5002 No H-bonds generated for 'chain 'D' and resid 5000 through 5002' Processing helix chain 'D' and resid 5005 through 5015 Processing helix chain 'D' and resid 5028 through 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 removed outlier: 3.784A pdb=" N PHE A4631 " --> pdb=" O LYS A4581 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER A4583 " --> pdb=" O TYR A4629 " (cutoff:3.500A) 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 removed outlier: 3.784A pdb=" N PHE B4631 " --> pdb=" O LYS B4581 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER B4583 " --> pdb=" O TYR B4629 " (cutoff:3.500A) 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 removed outlier: 3.784A pdb=" N PHE C4631 " --> pdb=" O LYS C4581 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER C4583 " --> pdb=" O TYR C4629 " (cutoff:3.500A) 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 removed outlier: 3.784A pdb=" N PHE D4631 " --> pdb=" O LYS D4581 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER D4583 " --> pdb=" O TYR D4629 " (cutoff:3.500A) 1190 hydrogen bonds defined for protein. 3102 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: 6.34 Time building geometry restraints manager: 9.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.37: 6715 1.37 - 1.52: 7056 1.52 - 1.66: 7073 1.66 - 1.80: 236 1.80 - 1.95: 44 Bond restraints: 21124 Sorted by residual: bond pdb=" CA LEU C4578 " pdb=" C LEU C4578 " ideal model delta sigma weight residual 1.523 1.545 -0.021 1.34e-02 5.57e+03 2.54e+00 bond pdb=" CA LEU B4578 " pdb=" C LEU B4578 " ideal model delta sigma weight residual 1.523 1.544 -0.021 1.34e-02 5.57e+03 2.34e+00 bond pdb=" CA LEU D4578 " pdb=" C LEU D4578 " ideal model delta sigma weight residual 1.523 1.543 -0.020 1.34e-02 5.57e+03 2.28e+00 bond pdb=" CA LEU A4578 " pdb=" C LEU A4578 " ideal model delta sigma weight residual 1.523 1.543 -0.020 1.34e-02 5.57e+03 2.28e+00 bond pdb=" N VAL C3990 " pdb=" CA VAL C3990 " ideal model delta sigma weight residual 1.474 1.456 0.019 1.57e-02 4.06e+03 1.41e+00 ... (remaining 21119 not shown) Histogram of bond angle deviations from ideal: 99.53 - 106.42: 472 106.42 - 113.31: 11030 113.31 - 120.20: 7956 120.20 - 127.09: 8890 127.09 - 133.98: 188 Bond angle restraints: 28536 Sorted by residual: angle pdb=" CB LYS C4060 " pdb=" CG LYS C4060 " pdb=" CD LYS C4060 " ideal model delta sigma weight residual 111.30 118.63 -7.33 2.30e+00 1.89e-01 1.02e+01 angle pdb=" CB LYS A4060 " pdb=" CG LYS A4060 " pdb=" CD LYS A4060 " ideal model delta sigma weight residual 111.30 118.59 -7.29 2.30e+00 1.89e-01 1.00e+01 angle pdb=" CB LYS B4060 " pdb=" CG LYS B4060 " pdb=" CD LYS B4060 " ideal model delta sigma weight residual 111.30 118.59 -7.29 2.30e+00 1.89e-01 1.00e+01 angle pdb=" CB LYS D4060 " pdb=" CG LYS D4060 " pdb=" CD LYS D4060 " ideal model delta sigma weight residual 111.30 118.58 -7.28 2.30e+00 1.89e-01 1.00e+01 angle pdb=" C VAL C3989 " pdb=" N VAL C3990 " pdb=" CA VAL C3990 " ideal model delta sigma weight residual 121.65 118.96 2.69 9.40e-01 1.13e+00 8.19e+00 ... (remaining 28531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.52: 11984 29.52 - 59.05: 392 59.05 - 88.57: 48 88.57 - 118.09: 4 118.09 - 147.62: 4 Dihedral angle restraints: 12432 sinusoidal: 5120 harmonic: 7312 Sorted by residual: dihedral pdb=" CA GLY C3971 " pdb=" C GLY C3971 " pdb=" N PRO C3972 " pdb=" CA PRO C3972 " ideal model delta harmonic sigma weight residual -180.00 -157.28 -22.72 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA GLY D3971 " pdb=" C GLY D3971 " pdb=" N PRO D3972 " pdb=" CA PRO D3972 " ideal model delta harmonic sigma weight residual -180.00 -157.30 -22.70 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA GLY B3971 " pdb=" C GLY B3971 " pdb=" N PRO B3972 " pdb=" CA PRO B3972 " ideal model delta harmonic sigma weight residual -180.00 -157.30 -22.70 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 12429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2147 0.034 - 0.068: 739 0.068 - 0.102: 146 0.102 - 0.136: 48 0.136 - 0.170: 4 Chirality restraints: 3084 Sorted by residual: chirality pdb=" CA GLU B4640 " pdb=" N GLU B4640 " pdb=" C GLU B4640 " pdb=" CB GLU B4640 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.24e-01 chirality pdb=" CA GLU A4640 " pdb=" N GLU A4640 " pdb=" C GLU A4640 " pdb=" CB GLU A4640 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.24e-01 chirality pdb=" CA GLU D4640 " pdb=" N GLU D4640 " pdb=" C GLU D4640 " pdb=" CB GLU D4640 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.24e-01 ... (remaining 3081 not shown) Planarity restraints: 3596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU D4244 " -0.007 2.00e-02 2.50e+03 1.40e-02 1.96e+00 pdb=" CD GLU D4244 " 0.024 2.00e-02 2.50e+03 pdb=" OE1 GLU D4244 " -0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU D4244 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C4244 " 0.007 2.00e-02 2.50e+03 1.40e-02 1.96e+00 pdb=" CD GLU C4244 " -0.024 2.00e-02 2.50e+03 pdb=" OE1 GLU C4244 " 0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU C4244 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A4244 " -0.007 2.00e-02 2.50e+03 1.40e-02 1.96e+00 pdb=" CD GLU A4244 " 0.024 2.00e-02 2.50e+03 pdb=" OE1 GLU A4244 " -0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU A4244 " -0.009 2.00e-02 2.50e+03 ... (remaining 3593 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3905 2.77 - 3.30: 20598 3.30 - 3.83: 34475 3.83 - 4.37: 39742 4.37 - 4.90: 68185 Nonbonded interactions: 166905 Sorted by model distance: nonbonded pdb=" NE1 TRP C3986 " pdb=" OE1 GLN C4043 " model vdw 2.236 2.520 nonbonded pdb=" NE1 TRP D3986 " pdb=" OE1 GLN D4043 " model vdw 2.237 2.520 nonbonded pdb=" O PHE A3992 " pdb=" N PHE A3996 " model vdw 2.238 2.520 nonbonded pdb=" O PHE B3992 " pdb=" N PHE B3996 " model vdw 2.238 2.520 nonbonded pdb=" O PHE D3992 " pdb=" N PHE D3996 " model vdw 2.241 2.520 ... (remaining 166900 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: 4.380 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: 14.670 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 58.200 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 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 : 0.003 0.041 21124 Z= 0.180 Angle : 0.532 7.335 28536 Z= 0.301 Chirality : 0.037 0.170 3084 Planarity : 0.003 0.035 3596 Dihedral : 14.621 147.616 7708 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.17), residues: 2464 helix: 1.82 (0.12), residues: 1680 sheet: -0.07 (0.76), residues: 64 loop : -0.19 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A3986 HIS 0.002 0.001 HIS C4803 PHE 0.022 0.001 PHE C4571 TYR 0.012 0.001 TYR C4580 ARG 0.003 0.000 ARG B4892 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 412 time to evaluate : 1.915 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 412 average time/residue: 0.3094 time to fit residues: 198.5244 Evaluate side-chains 361 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 361 time to evaluate : 2.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 126 optimal weight: 0.0670 chunk 100 optimal weight: 4.9990 chunk 194 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 118 optimal weight: 0.0670 chunk 144 optimal weight: 0.2980 chunk 225 optimal weight: 0.9990 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4020 GLN B4020 GLN C3994 HIS C4020 GLN D3994 HIS D4020 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21124 Z= 0.142 Angle : 0.478 6.995 28536 Z= 0.260 Chirality : 0.036 0.138 3084 Planarity : 0.004 0.035 3596 Dihedral : 9.324 149.655 2776 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % 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: 2.04 (0.17), residues: 2464 helix: 1.81 (0.12), residues: 1728 sheet: 0.70 (0.57), residues: 104 loop : 0.35 (0.28), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C3986 HIS 0.006 0.001 HIS D3994 PHE 0.010 0.001 PHE A4631 TYR 0.010 0.001 TYR A4629 ARG 0.004 0.000 ARG C4736 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 380 time to evaluate : 2.274 Fit side-chains REVERT: A 4690 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8222 (tp30) REVERT: A 4798 MET cc_start: 0.8083 (mmm) cc_final: 0.7823 (mmm) REVERT: B 4690 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8222 (tp30) REVERT: B 4798 MET cc_start: 0.8084 (mmm) cc_final: 0.7826 (mmm) REVERT: C 4690 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8244 (tp30) REVERT: C 4798 MET cc_start: 0.8084 (mmm) cc_final: 0.7830 (mmm) REVERT: D 4690 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8230 (tp30) REVERT: D 4798 MET cc_start: 0.8084 (mmm) cc_final: 0.7828 (mmm) outliers start: 0 outliers final: 0 residues processed: 380 average time/residue: 0.3227 time to fit residues: 195.2453 Evaluate side-chains 360 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 360 time to evaluate : 2.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 62 optimal weight: 20.0000 chunk 225 optimal weight: 0.9980 chunk 243 optimal weight: 6.9990 chunk 200 optimal weight: 0.9980 chunk 223 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 180 optimal weight: 0.7980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3994 HIS B3994 HIS C3994 HIS D3994 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21124 Z= 0.262 Angle : 0.518 7.161 28536 Z= 0.278 Chirality : 0.039 0.188 3084 Planarity : 0.004 0.038 3596 Dihedral : 9.347 148.571 2776 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.36 % Allowed : 9.68 % Favored : 89.96 % 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: 1.64 (0.17), residues: 2464 helix: 1.58 (0.12), residues: 1700 sheet: 0.60 (0.57), residues: 104 loop : 0.04 (0.27), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B3986 HIS 0.005 0.001 HIS A3994 PHE 0.013 0.001 PHE C4921 TYR 0.013 0.002 TYR D4580 ARG 0.005 0.000 ARG C4892 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 369 time to evaluate : 2.280 Fit side-chains REVERT: A 3957 VAL cc_start: 0.8371 (t) cc_final: 0.8122 (p) REVERT: B 3957 VAL cc_start: 0.8350 (t) cc_final: 0.8102 (p) REVERT: C 3957 VAL cc_start: 0.8357 (t) cc_final: 0.8120 (p) REVERT: D 3957 VAL cc_start: 0.8373 (t) cc_final: 0.8133 (p) outliers start: 8 outliers final: 0 residues processed: 369 average time/residue: 0.2891 time to fit residues: 168.6288 Evaluate side-chains 346 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 346 time to evaluate : 2.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 0.3980 chunk 169 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 151 optimal weight: 0.7980 chunk 226 optimal weight: 0.8980 chunk 239 optimal weight: 4.9990 chunk 118 optimal weight: 0.0970 chunk 214 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3994 HIS B3994 HIS C3994 HIS D3994 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21124 Z= 0.134 Angle : 0.444 7.008 28536 Z= 0.242 Chirality : 0.035 0.133 3084 Planarity : 0.004 0.035 3596 Dihedral : 9.214 151.353 2776 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.63 % Allowed : 10.89 % Favored : 88.49 % 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: 1.79 (0.17), residues: 2464 helix: 1.78 (0.12), residues: 1696 sheet: 0.74 (0.57), residues: 104 loop : -0.21 (0.26), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C4644 HIS 0.005 0.001 HIS A3994 PHE 0.007 0.001 PHE A4631 TYR 0.013 0.001 TYR B4638 ARG 0.003 0.000 ARG D4892 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 344 time to evaluate : 2.337 Fit side-chains REVERT: A 3957 VAL cc_start: 0.8362 (t) cc_final: 0.8079 (p) REVERT: A 4851 TYR cc_start: 0.7456 (m-80) cc_final: 0.7055 (m-80) REVERT: B 3957 VAL cc_start: 0.8339 (t) cc_final: 0.8060 (p) REVERT: B 4851 TYR cc_start: 0.7384 (m-80) cc_final: 0.6958 (m-80) REVERT: C 3957 VAL cc_start: 0.8346 (t) cc_final: 0.8058 (p) REVERT: C 3986 TRP cc_start: 0.8108 (m100) cc_final: 0.6824 (m100) REVERT: C 4851 TYR cc_start: 0.7458 (m-80) cc_final: 0.7054 (m-80) REVERT: D 3957 VAL cc_start: 0.8363 (t) cc_final: 0.8071 (p) REVERT: D 3986 TRP cc_start: 0.8118 (m100) cc_final: 0.6830 (m100) REVERT: D 4851 TYR cc_start: 0.7462 (m-80) cc_final: 0.7059 (m-80) outliers start: 14 outliers final: 6 residues processed: 354 average time/residue: 0.3101 time to fit residues: 174.2645 Evaluate side-chains 340 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 334 time to evaluate : 2.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain C residue 4025 VAL Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain D residue 4025 VAL Chi-restraints excluded: chain D residue 4666 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 7.9990 chunk 136 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 178 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 204 optimal weight: 0.0770 chunk 165 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 122 optimal weight: 4.9990 chunk 215 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 overall best weight: 2.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3994 HIS ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3994 HIS B4886 HIS C3994 HIS D3994 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 21124 Z= 0.350 Angle : 0.561 7.181 28536 Z= 0.297 Chirality : 0.040 0.138 3084 Planarity : 0.004 0.037 3596 Dihedral : 9.302 148.785 2776 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.54 % Allowed : 13.13 % Favored : 86.34 % 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: 1.23 (0.17), residues: 2464 helix: 1.32 (0.12), residues: 1700 sheet: 0.69 (0.57), residues: 104 loop : -0.36 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B3986 HIS 0.006 0.001 HIS D3994 PHE 0.015 0.002 PHE D4921 TYR 0.018 0.002 TYR B4580 ARG 0.005 0.000 ARG A4892 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 333 time to evaluate : 2.353 Fit side-chains REVERT: A 4852 THR cc_start: 0.7367 (m) cc_final: 0.7125 (m) REVERT: C 3957 VAL cc_start: 0.8334 (t) cc_final: 0.8092 (p) REVERT: C 4852 THR cc_start: 0.7410 (m) cc_final: 0.7150 (m) REVERT: D 3957 VAL cc_start: 0.8350 (t) cc_final: 0.8105 (p) REVERT: D 4852 THR cc_start: 0.7411 (m) cc_final: 0.7155 (m) outliers start: 12 outliers final: 8 residues processed: 341 average time/residue: 0.3091 time to fit residues: 168.5178 Evaluate side-chains 327 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 319 time to evaluate : 2.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain C residue 3987 ASP Chi-restraints excluded: chain C residue 4025 VAL Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain D residue 3987 ASP Chi-restraints excluded: chain D residue 4025 VAL Chi-restraints excluded: chain D residue 4666 VAL 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: 0.8980 chunk 47 optimal weight: 0.7980 chunk 140 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 239 optimal weight: 1.9990 chunk 199 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 125 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3994 HIS B3994 HIS C3994 HIS D3994 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21124 Z= 0.178 Angle : 0.471 7.018 28536 Z= 0.255 Chirality : 0.036 0.130 3084 Planarity : 0.004 0.036 3596 Dihedral : 9.226 151.393 2776 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.49 % Allowed : 14.02 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.17), residues: 2464 helix: 1.49 (0.12), residues: 1704 sheet: 0.81 (0.58), residues: 104 loop : -0.33 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B4794 HIS 0.004 0.001 HIS A3994 PHE 0.009 0.001 PHE D4921 TYR 0.010 0.001 TYR C4580 ARG 0.003 0.000 ARG C4892 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 322 time to evaluate : 2.526 Fit side-chains REVERT: A 4047 MET cc_start: 0.7960 (tmm) cc_final: 0.7700 (tpt) REVERT: B 4047 MET cc_start: 0.7962 (tmm) cc_final: 0.7701 (tpt) outliers start: 11 outliers final: 7 residues processed: 330 average time/residue: 0.3047 time to fit residues: 159.5512 Evaluate side-chains 321 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 314 time to evaluate : 2.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain B residue 4025 VAL Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain C residue 4025 VAL Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain D residue 4025 VAL Chi-restraints excluded: chain D residue 4666 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 136 optimal weight: 7.9990 chunk 175 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 201 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 239 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3994 HIS ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4886 HIS B3994 HIS ** B4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3994 HIS C4886 HIS D3994 HIS D4886 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 21124 Z= 0.305 Angle : 0.530 7.166 28536 Z= 0.283 Chirality : 0.039 0.129 3084 Planarity : 0.004 0.038 3596 Dihedral : 9.211 149.416 2776 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.45 % Allowed : 14.25 % Favored : 85.30 % 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: 1.12 (0.17), residues: 2464 helix: 1.25 (0.12), residues: 1700 sheet: 0.48 (0.58), residues: 104 loop : -0.39 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B4794 HIS 0.006 0.001 HIS A3994 PHE 0.013 0.001 PHE B4921 TYR 0.016 0.002 TYR C4580 ARG 0.004 0.000 ARG B4892 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 317 time to evaluate : 2.757 Fit side-chains REVERT: A 4212 GLU cc_start: 0.7276 (tp30) cc_final: 0.6947 (tp30) REVERT: A 4852 THR cc_start: 0.7414 (m) cc_final: 0.7002 (p) REVERT: B 4212 GLU cc_start: 0.7274 (tp30) cc_final: 0.6948 (tp30) REVERT: C 4212 GLU cc_start: 0.7282 (tp30) cc_final: 0.6950 (tp30) REVERT: C 4852 THR cc_start: 0.7456 (m) cc_final: 0.7021 (p) REVERT: D 4212 GLU cc_start: 0.7277 (tp30) cc_final: 0.6951 (tp30) REVERT: D 4852 THR cc_start: 0.7452 (m) cc_final: 0.7019 (p) outliers start: 10 outliers final: 10 residues processed: 325 average time/residue: 0.3216 time to fit residues: 165.1888 Evaluate side-chains 320 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 310 time to evaluate : 2.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3985 LEU Chi-restraints excluded: chain A residue 4025 VAL Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain B residue 3985 LEU Chi-restraints excluded: chain B residue 4025 VAL Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain C residue 4025 VAL Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain D residue 4025 VAL Chi-restraints excluded: chain D residue 4666 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 0.8980 chunk 95 optimal weight: 0.4980 chunk 142 optimal weight: 5.9990 chunk 72 optimal weight: 0.1980 chunk 46 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 118 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 chunk 217 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3994 HIS ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3994 HIS ** B4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3994 HIS D3994 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21124 Z= 0.161 Angle : 0.462 6.960 28536 Z= 0.250 Chirality : 0.036 0.131 3084 Planarity : 0.004 0.036 3596 Dihedral : 9.076 151.585 2776 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.36 % Allowed : 14.78 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.17), residues: 2464 helix: 1.54 (0.13), residues: 1684 sheet: 0.75 (0.59), residues: 104 loop : -0.34 (0.25), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B4644 HIS 0.004 0.001 HIS B3994 PHE 0.008 0.001 PHE B4916 TYR 0.009 0.001 TYR A4580 ARG 0.003 0.000 ARG C4892 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 336 time to evaluate : 2.448 Fit side-chains REVERT: A 4212 GLU cc_start: 0.7151 (tp30) cc_final: 0.6837 (tp30) REVERT: A 4851 TYR cc_start: 0.7525 (m-80) cc_final: 0.7059 (m-80) REVERT: A 5013 MET cc_start: 0.8552 (mmm) cc_final: 0.8115 (mmm) REVERT: B 4212 GLU cc_start: 0.7147 (tp30) cc_final: 0.6835 (tp30) REVERT: B 4851 TYR cc_start: 0.7281 (m-80) cc_final: 0.6826 (m-80) REVERT: B 5013 MET cc_start: 0.8558 (mmm) cc_final: 0.8112 (mmm) REVERT: C 3986 TRP cc_start: 0.8175 (m100) cc_final: 0.7089 (m100) REVERT: C 4212 GLU cc_start: 0.7159 (tp30) cc_final: 0.6839 (tp30) REVERT: C 4851 TYR cc_start: 0.7524 (m-80) cc_final: 0.7049 (m-80) REVERT: C 5013 MET cc_start: 0.8546 (mmm) cc_final: 0.8107 (mmm) REVERT: D 3986 TRP cc_start: 0.8186 (m100) cc_final: 0.7104 (m100) REVERT: D 4212 GLU cc_start: 0.7153 (tp30) cc_final: 0.6841 (tp30) REVERT: D 4851 TYR cc_start: 0.7525 (m-80) cc_final: 0.7058 (m-80) REVERT: D 5013 MET cc_start: 0.8550 (mmm) cc_final: 0.8111 (mmm) outliers start: 8 outliers final: 8 residues processed: 340 average time/residue: 0.3007 time to fit residues: 162.3889 Evaluate side-chains 339 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 331 time to evaluate : 2.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4025 VAL Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain B residue 4025 VAL Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain C residue 4025 VAL Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain D residue 4025 VAL Chi-restraints excluded: chain D residue 4666 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 0.9980 chunk 208 optimal weight: 0.6980 chunk 222 optimal weight: 5.9990 chunk 134 optimal weight: 10.0000 chunk 97 optimal weight: 0.9980 chunk 174 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 201 optimal weight: 4.9990 chunk 210 optimal weight: 0.9990 chunk 221 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3994 HIS ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3994 HIS ** B4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3994 HIS D3994 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21124 Z= 0.170 Angle : 0.469 6.976 28536 Z= 0.251 Chirality : 0.036 0.125 3084 Planarity : 0.004 0.035 3596 Dihedral : 8.896 150.017 2776 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.45 % Allowed : 15.37 % Favored : 84.18 % 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: 1.52 (0.17), residues: 2464 helix: 1.58 (0.13), residues: 1680 sheet: 0.83 (0.60), residues: 104 loop : -0.31 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A4644 HIS 0.006 0.001 HIS D3994 PHE 0.008 0.001 PHE D4916 TYR 0.010 0.001 TYR B4630 ARG 0.003 0.000 ARG C4892 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 334 time to evaluate : 2.304 Fit side-chains REVERT: A 4212 GLU cc_start: 0.7117 (tp30) cc_final: 0.6768 (tp30) REVERT: A 4879 MET cc_start: 0.7264 (tpp) cc_final: 0.6956 (tpt) REVERT: A 5013 MET cc_start: 0.8527 (mmm) cc_final: 0.8061 (mmm) REVERT: B 3986 TRP cc_start: 0.7916 (m100) cc_final: 0.7509 (m100) REVERT: B 4212 GLU cc_start: 0.7112 (tp30) cc_final: 0.6765 (tp30) REVERT: B 5013 MET cc_start: 0.8534 (mmm) cc_final: 0.8057 (mmm) REVERT: C 4212 GLU cc_start: 0.7126 (tp30) cc_final: 0.6770 (tp30) REVERT: C 4879 MET cc_start: 0.7263 (tpp) cc_final: 0.6973 (tpt) REVERT: C 5013 MET cc_start: 0.8521 (mmm) cc_final: 0.8056 (mmm) REVERT: D 4212 GLU cc_start: 0.7118 (tp30) cc_final: 0.6771 (tp30) REVERT: D 4879 MET cc_start: 0.7259 (tpp) cc_final: 0.6962 (tpt) REVERT: D 5013 MET cc_start: 0.8527 (mmm) cc_final: 0.8058 (mmm) outliers start: 10 outliers final: 10 residues processed: 340 average time/residue: 0.3071 time to fit residues: 165.8691 Evaluate side-chains 339 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 329 time to evaluate : 2.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3985 LEU Chi-restraints excluded: chain A residue 4025 VAL Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain B residue 3985 LEU Chi-restraints excluded: chain B residue 4025 VAL Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain C residue 4025 VAL Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain D residue 4025 VAL Chi-restraints excluded: chain D residue 4666 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 235 optimal weight: 0.0000 chunk 143 optimal weight: 0.1980 chunk 111 optimal weight: 0.0020 chunk 163 optimal weight: 0.6980 chunk 247 optimal weight: 2.9990 chunk 227 optimal weight: 0.9980 chunk 196 optimal weight: 8.9990 chunk 20 optimal weight: 0.0470 chunk 151 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 overall best weight: 0.1890 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3994 HIS ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3994 HIS C3994 HIS D3994 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21124 Z= 0.118 Angle : 0.446 7.585 28536 Z= 0.240 Chirality : 0.035 0.136 3084 Planarity : 0.003 0.032 3596 Dihedral : 8.598 151.113 2776 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.27 % Allowed : 15.55 % Favored : 84.18 % 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: 1.80 (0.17), residues: 2464 helix: 1.77 (0.13), residues: 1700 sheet: 0.86 (0.57), residues: 104 loop : -0.17 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B4644 HIS 0.006 0.001 HIS A3994 PHE 0.007 0.001 PHE A4671 TYR 0.009 0.001 TYR D4888 ARG 0.004 0.000 ARG D4892 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 370 time to evaluate : 2.453 Fit side-chains REVERT: A 3986 TRP cc_start: 0.7725 (m100) cc_final: 0.7201 (m100) REVERT: A 4672 LYS cc_start: 0.7982 (mtpp) cc_final: 0.7674 (mtmt) REVERT: A 4851 TYR cc_start: 0.7488 (m-80) cc_final: 0.7098 (m-80) REVERT: A 4879 MET cc_start: 0.7380 (tpp) cc_final: 0.6939 (tpt) REVERT: A 5013 MET cc_start: 0.8522 (mmm) cc_final: 0.8099 (mmm) REVERT: B 4672 LYS cc_start: 0.7981 (mtpp) cc_final: 0.7670 (mtmt) REVERT: B 4851 TYR cc_start: 0.7339 (m-80) cc_final: 0.6895 (m-80) REVERT: B 5013 MET cc_start: 0.8530 (mmm) cc_final: 0.8096 (mmm) REVERT: C 3986 TRP cc_start: 0.8144 (m100) cc_final: 0.7087 (m100) REVERT: C 4672 LYS cc_start: 0.7979 (mtpp) cc_final: 0.7674 (mtmt) REVERT: C 4851 TYR cc_start: 0.7483 (m-80) cc_final: 0.7091 (m-80) REVERT: C 4879 MET cc_start: 0.7376 (tpp) cc_final: 0.6953 (tpt) REVERT: C 5013 MET cc_start: 0.8514 (mmm) cc_final: 0.8092 (mmm) REVERT: D 4672 LYS cc_start: 0.7983 (mtpp) cc_final: 0.7670 (mtmt) REVERT: D 4851 TYR cc_start: 0.7484 (m-80) cc_final: 0.7096 (m-80) REVERT: D 4879 MET cc_start: 0.7375 (tpp) cc_final: 0.6943 (tpt) REVERT: D 5013 MET cc_start: 0.8521 (mmm) cc_final: 0.8097 (mmm) outliers start: 6 outliers final: 6 residues processed: 372 average time/residue: 0.3083 time to fit residues: 181.1224 Evaluate side-chains 349 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 343 time to evaluate : 2.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3985 LEU Chi-restraints excluded: chain A residue 4025 VAL Chi-restraints excluded: chain B residue 3985 LEU Chi-restraints excluded: chain B residue 4025 VAL Chi-restraints excluded: chain C residue 4025 VAL Chi-restraints excluded: chain D residue 4025 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 0.0020 chunk 60 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 197 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 202 optimal weight: 0.3980 chunk 24 optimal weight: 0.0970 chunk 36 optimal weight: 0.6980 chunk 173 optimal weight: 0.0020 overall best weight: 0.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3994 HIS ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3994 HIS ** B4043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3994 HIS D3994 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.157826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.125330 restraints weight = 29640.021| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.87 r_work: 0.3343 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21124 Z= 0.123 Angle : 0.456 7.037 28536 Z= 0.242 Chirality : 0.035 0.128 3084 Planarity : 0.003 0.031 3596 Dihedral : 8.301 148.207 2776 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.27 % Allowed : 15.77 % Favored : 83.96 % 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: 1.89 (0.17), residues: 2464 helix: 1.82 (0.13), residues: 1704 sheet: 0.93 (0.56), residues: 104 loop : -0.11 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B4644 HIS 0.007 0.001 HIS A3994 PHE 0.006 0.001 PHE A4671 TYR 0.009 0.001 TYR B4888 ARG 0.004 0.000 ARG D4892 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4727.42 seconds wall clock time: 86 minutes 44.48 seconds (5204.48 seconds total)