Starting phenix.real_space_refine on Thu Jul 2 15:14:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8es7_28570/07_2026/8es7_28570.cif Found real_map, /net/cci-nas-00/data/ceres_data/8es7_28570/07_2026/8es7_28570.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8es7_28570/07_2026/8es7_28570.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8es7_28570/07_2026/8es7_28570.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8es7_28570/07_2026/8es7_28570.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8es7_28570/07_2026/8es7_28570.cif" model { file = "/net/cci-nas-00/data/ceres_data/8es7_28570/07_2026/8es7_28570.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8es7_28570/07_2026/8es7_28570.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= -0.000 sd= 1.000 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: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 5624 2.51 5 N 1420 2.21 5 O 1723 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8822 Number of models: 1 Model: "" Number of chains: 18 Chain: "Z" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 286 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 34} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Y" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 249 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "D" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain: "F" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain: "G" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 913 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "E" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 978 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "A" Number of atoms: 2002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2002 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain: "B" Number of atoms: 2292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2292 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 273} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.10, per 1000 atoms: 0.24 Number of scatterers: 8822 At special positions: 0 Unit cell: (88.4, 92.65, 148.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 55 16.00 O 1723 8.00 N 1420 7.00 C 5624 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS Z 32 " - pdb=" SG CYS Y 32 " distance=2.04 Simple disulfide: pdb=" SG CYS D 37 " - pdb=" SG CYS D 73 " distance=2.04 Simple disulfide: pdb=" SG CYS D 93 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 49 " - pdb=" SG CYS F 98 " distance=2.04 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 122 " distance=2.03 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 87 " distance=2.03 Simple disulfide: pdb=" SG CYS G 104 " - pdb=" SG CYS G 107 " distance=2.04 Simple disulfide: pdb=" SG CYS E 49 " - pdb=" SG CYS E 98 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 122 " distance=2.03 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 190 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS B 245 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 91 " distance=2.03 Simple disulfide: pdb=" SG CYS B 145 " - pdb=" SG CYS B 210 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG H 1 " - " NAG H 2 " " NAG J 1 " - " NAG J 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " NAG-ASN " NAG A 301 " - " ASN A 184 " " NAG A 302 " - " ASN A 195 " " NAG B1701 " - " ASN B 184 " " NAG C 1 " - " ASN D 38 " " NAG G1701 " - " ASN G 92 " " NAG G1702 " - " ASN G 52 " " NAG H 1 " - " ASN B 84 " " NAG J 1 " - " ASN A 58 " " NAG N 1 " - " ASN A 150 " " NAG O 1 " - " ASN D 74 " " NAG P 1 " - " ASN B 107 " Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 460.7 milliseconds 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2014 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 21 sheets defined 28.6% alpha, 32.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'Z' and resid 29 through 57 removed outlier: 3.591A pdb=" N TYR Z 33 " --> pdb=" O PRO Z 29 " (cutoff:3.500A) Processing helix chain 'Y' and resid 28 through 55 removed outlier: 4.361A pdb=" N CYS Y 32 " --> pdb=" O ASP Y 28 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE Y 41 " --> pdb=" O GLY Y 37 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE Y 55 " --> pdb=" O LEU Y 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 128 removed outlier: 3.978A pdb=" N GLY D 127 " --> pdb=" O PHE D 123 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N HIS D 128 " --> pdb=" O CYS D 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 93 Processing helix chain 'F' and resid 104 through 108 Processing helix chain 'F' and resid 126 through 156 Processing helix chain 'G' and resid 78 through 80 No H-bonds generated for 'chain 'G' and resid 78 through 80' Processing helix chain 'G' and resid 111 through 136 removed outlier: 3.513A pdb=" N ILE G 115 " --> pdb=" O ASN G 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 93 removed outlier: 3.683A pdb=" N SER E 93 " --> pdb=" O GLU E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 155 removed outlier: 3.521A pdb=" N VAL E 130 " --> pdb=" O ASP E 126 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASN E 154 " --> pdb=" O TYR E 150 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ARG E 155 " --> pdb=" O TRP E 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 87 removed outlier: 3.611A pdb=" N ASP A 86 " --> pdb=" O GLN A 83 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER A 87 " --> pdb=" O LEU A 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 83 through 87' Processing helix chain 'A' and resid 192 through 196 removed outlier: 4.669A pdb=" N ASN A 196 " --> pdb=" O ALA A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 220 removed outlier: 3.830A pdb=" N SER A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 255 Processing helix chain 'B' and resid 82 through 86 removed outlier: 3.750A pdb=" N THR B 86 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 120 removed outlier: 3.544A pdb=" N LYS B 119 " --> pdb=" O ASP B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 139 Processing helix chain 'B' and resid 198 through 202 Processing helix chain 'B' and resid 248 through 289 removed outlier: 3.803A pdb=" N LYS B 289 " --> pdb=" O MET B 285 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 26 through 27 removed outlier: 5.955A pdb=" N VAL D 33 " --> pdb=" O LEU D 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 42 through 46 removed outlier: 6.478A pdb=" N ILE D 70 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR D 85 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N TYR E 113 " --> pdb=" O THR D 85 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLN D 87 " --> pdb=" O TYR E 113 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ARG E 115 " --> pdb=" O GLN D 87 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N HIS D 89 " --> pdb=" O ARG E 115 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N PHE E 110 " --> pdb=" O CYS E 98 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N CYS E 98 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N TRP E 59 " --> pdb=" O ILE E 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'F' and resid 37 through 41 removed outlier: 3.527A pdb=" N THR F 44 " --> pdb=" O SER F 41 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N HIS F 81 " --> pdb=" O ASP F 78 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASP F 78 " --> pdb=" O HIS F 81 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 64 through 66 removed outlier: 4.060A pdb=" N TRP F 59 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE G 53 " --> pdb=" O PHE G 64 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N PHE G 64 " --> pdb=" O ILE G 53 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TRP G 55 " --> pdb=" O ILE G 62 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 122 through 124 Processing sheet with id=AA7, first strand: chain 'G' and resid 31 through 34 removed outlier: 3.502A pdb=" N LEU G 43 " --> pdb=" O TYR G 34 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL G 42 " --> pdb=" O LEU G 74 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 37 through 41 removed outlier: 3.597A pdb=" N LYS E 37 " --> pdb=" O THR E 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 3 through 5 Processing sheet with id=AB1, first strand: chain 'A' and resid 11 through 14 removed outlier: 6.588A pdb=" N MET A 11 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N HIS A 116 " --> pdb=" O MET A 11 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL A 13 " --> pdb=" O HIS A 116 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 49 " --> pdb=" O TRP A 36 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LYS A 38 " --> pdb=" O PHE A 47 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N PHE A 47 " --> pdb=" O LYS A 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 11 through 14 removed outlier: 6.588A pdb=" N MET A 11 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N HIS A 116 " --> pdb=" O MET A 11 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL A 13 " --> pdb=" O HIS A 116 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 19 through 21 Processing sheet with id=AB4, first strand: chain 'A' and resid 125 through 128 Processing sheet with id=AB5, first strand: chain 'A' and resid 125 through 128 Processing sheet with id=AB6, first strand: chain 'B' and resid 4 through 6 Processing sheet with id=AB7, first strand: chain 'B' and resid 10 through 14 removed outlier: 6.520A pdb=" N LEU B 11 " --> pdb=" O THR B 112 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N THR B 114 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LYS B 13 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET B 88 " --> pdb=" O GLN B 37 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ARG B 36 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LEU B 45 " --> pdb=" O ARG B 36 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ASP B 38 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N LEU B 43 " --> pdb=" O ASP B 38 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 10 through 14 removed outlier: 6.520A pdb=" N LEU B 11 " --> pdb=" O THR B 112 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N THR B 114 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LYS B 13 " --> pdb=" O THR B 114 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 19 through 21 Processing sheet with id=AC1, first strand: chain 'B' and resid 124 through 128 removed outlier: 5.691A pdb=" N TYR B 188 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 124 through 128 removed outlier: 5.691A pdb=" N TYR B 188 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 164 through 165 447 hydrogen bonds defined for protein. 1200 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: 1.35 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2773 1.34 - 1.47: 2235 1.47 - 1.59: 3922 1.59 - 1.71: 0 1.71 - 1.83: 78 Bond restraints: 9008 Sorted by residual: bond pdb=" CAI Y01 Y 201 " pdb=" CAK Y01 Y 201 " ideal model delta sigma weight residual 1.492 1.405 0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" CAI Y01 Y 201 " pdb=" CAZ Y01 Y 201 " ideal model delta sigma weight residual 1.332 1.381 -0.049 2.00e-02 2.50e+03 6.07e+00 bond pdb=" CAY Y01 Y 201 " pdb=" OAG Y01 Y 201 " ideal model delta sigma weight residual 1.207 1.250 -0.043 2.00e-02 2.50e+03 4.56e+00 bond pdb=" CBB Y01 Y 201 " pdb=" CBE Y01 Y 201 " ideal model delta sigma weight residual 1.535 1.573 -0.038 2.00e-02 2.50e+03 3.69e+00 bond pdb=" CAV Y01 Y 201 " pdb=" CAZ Y01 Y 201 " ideal model delta sigma weight residual 1.507 1.470 0.037 2.00e-02 2.50e+03 3.43e+00 ... (remaining 9003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 12010 2.40 - 4.81: 176 4.81 - 7.21: 16 7.21 - 9.62: 2 9.62 - 12.02: 2 Bond angle restraints: 12206 Sorted by residual: angle pdb=" OAG Y01 Y 201 " pdb=" CAY Y01 Y 201 " pdb=" OAW Y01 Y 201 " ideal model delta sigma weight residual 123.38 111.36 12.02 3.00e+00 1.11e-01 1.61e+01 angle pdb=" CAM Y01 Y 201 " pdb=" CAY Y01 Y 201 " pdb=" OAW Y01 Y 201 " ideal model delta sigma weight residual 111.19 122.99 -11.80 3.00e+00 1.11e-01 1.55e+01 angle pdb=" CAV Y01 Y 201 " pdb=" CAZ Y01 Y 201 " pdb=" CBH Y01 Y 201 " ideal model delta sigma weight residual 116.96 126.42 -9.46 3.00e+00 1.11e-01 9.94e+00 angle pdb=" CAV Y01 Y 201 " pdb=" CBC Y01 Y 201 " pdb=" OAW Y01 Y 201 " ideal model delta sigma weight residual 110.72 101.54 9.18 3.00e+00 1.11e-01 9.36e+00 angle pdb=" C MET A 172 " pdb=" N ASP A 173 " pdb=" CA ASP A 173 " ideal model delta sigma weight residual 121.54 127.31 -5.77 1.91e+00 2.74e-01 9.14e+00 ... (remaining 12201 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 4712 17.81 - 35.62: 415 35.62 - 53.44: 92 53.44 - 71.25: 21 71.25 - 89.06: 10 Dihedral angle restraints: 5250 sinusoidal: 2111 harmonic: 3139 Sorted by residual: dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 122 " pdb=" CB CYS E 122 " ideal model delta sinusoidal sigma weight residual 93.00 28.56 64.44 1 1.00e+01 1.00e-02 5.46e+01 dihedral pdb=" CB CYS A 140 " pdb=" SG CYS A 140 " pdb=" SG CYS A 190 " pdb=" CB CYS A 190 " ideal model delta sinusoidal sigma weight residual 93.00 153.35 -60.35 1 1.00e+01 1.00e-02 4.85e+01 dihedral pdb=" CB CYS D 93 " pdb=" SG CYS D 93 " pdb=" SG CYS D 96 " pdb=" CB CYS D 96 " ideal model delta sinusoidal sigma weight residual -86.00 -34.90 -51.10 1 1.00e+01 1.00e-02 3.57e+01 ... (remaining 5247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1247 0.070 - 0.139: 149 0.139 - 0.209: 13 0.209 - 0.278: 3 0.278 - 0.348: 3 Chirality restraints: 1415 Sorted by residual: chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN A 150 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN D 74 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CB ILE B 60 " pdb=" CA ILE B 60 " pdb=" CG1 ILE B 60 " pdb=" CG2 ILE B 60 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 1412 not shown) Planarity restraints: 1535 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS F 49 " 0.034 5.00e-02 4.00e+02 5.24e-02 4.40e+00 pdb=" N PRO F 50 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO F 50 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO F 50 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 52 " 0.032 5.00e-02 4.00e+02 4.82e-02 3.72e+00 pdb=" N PRO E 53 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO E 53 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 53 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 256 " -0.019 2.00e-02 2.50e+03 1.21e-02 3.66e+00 pdb=" CG TRP A 256 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP A 256 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP A 256 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 256 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 256 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 256 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 256 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 256 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 256 " -0.002 2.00e-02 2.50e+03 ... (remaining 1532 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 176 2.69 - 3.24: 8108 3.24 - 3.79: 13029 3.79 - 4.35: 17163 4.35 - 4.90: 29462 Nonbonded interactions: 67938 Sorted by model distance: nonbonded pdb=" OH TYR A 50 " pdb=" O TYR B 99 " model vdw 2.133 3.040 nonbonded pdb=" OG SER Z 23 " pdb=" OE1 GLN D 94 " model vdw 2.157 3.040 nonbonded pdb=" OE2 GLU D 28 " pdb=" OH TYR D 90 " model vdw 2.178 3.040 nonbonded pdb=" OG1 THR G 66 " pdb=" OD1 ASP G 68 " model vdw 2.216 3.040 nonbonded pdb=" OG1 THR A 27 " pdb=" OD1 ASP A 29 " model vdw 2.227 3.040 ... (remaining 67933 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'E' selection = (chain 'F' and resid 33 through 155) } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'N' selection = chain 'O' selection = chain 'P' } ncs_group { reference = (chain 'Y' and resid 25 through 55) selection = (chain 'Z' and resid 25 through 55) } 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: 0.010 Normalize map: mean=0, sd=1: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 9.290 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 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 0.087 9040 Z= 0.195 Angle : 0.717 12.021 12288 Z= 0.344 Chirality : 0.048 0.348 1415 Planarity : 0.004 0.052 1524 Dihedral : 14.514 89.058 3194 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.10 % Allowed : 0.31 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.27), residues: 1064 helix: 3.45 (0.30), residues: 266 sheet: 1.08 (0.30), residues: 310 loop : -1.56 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Y 52 TYR 0.025 0.001 TYR G 34 PHE 0.018 0.001 PHE G 135 TRP 0.031 0.001 TRP A 256 HIS 0.004 0.001 HIS F 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 ( 9008) covalent geometry : angle 0.68131 / 0.34 (12206) SS BOND : bond 0.00361 / 0.20 ( 14) SS BOND : angle 1.67730 / 1.18 ( 28) hydrogen bonds : bond 0.12180 / 7.92 ( 416) hydrogen bonds : angle 5.08934 / 3.42 ( 1200) link_BETA1-4 : bond 0.00277 / 0.15 ( 7) link_BETA1-4 : angle 1.23746 / 0.74 ( 21) link_NAG-ASN : bond 0.00690 / 0.33 ( 11) link_NAG-ASN : angle 4.01699 / 2.58 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 165 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: D 78 ILE cc_start: 0.9036 (pt) cc_final: 0.8613 (pt) REVERT: B 50 TYR cc_start: 0.8090 (t80) cc_final: 0.7694 (t80) outliers start: 1 outliers final: 0 residues processed: 165 average time/residue: 0.0940 time to fit residues: 21.5747 Evaluate side-chains 137 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 121 ASN G 23 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.136517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.096626 restraints weight = 11644.292| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.07 r_work: 0.2947 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.0867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9040 Z= 0.160 Angle : 0.637 9.346 12288 Z= 0.321 Chirality : 0.044 0.258 1415 Planarity : 0.003 0.041 1524 Dihedral : 4.961 51.155 1179 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.15 % Allowed : 8.28 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.27), residues: 1064 helix: 3.37 (0.30), residues: 270 sheet: 1.10 (0.30), residues: 303 loop : -1.52 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 101 TYR 0.013 0.001 TYR A 37 PHE 0.018 0.001 PHE Z 40 TRP 0.010 0.001 TRP A 182 HIS 0.005 0.001 HIS E 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 9008) covalent geometry : angle 0.60214 / 0.31 (12206) SS BOND : bond 0.00758 / 0.37 ( 14) SS BOND : angle 1.34932 / 0.85 ( 28) hydrogen bonds : bond 0.05021 / 3.27 ( 416) hydrogen bonds : angle 4.22939 / 2.83 ( 1200) link_BETA1-4 : bond 0.00340 / 0.16 ( 7) link_BETA1-4 : angle 1.38659 / 0.84 ( 21) link_NAG-ASN : bond 0.00639 / 0.37 ( 11) link_NAG-ASN : angle 3.79586 / 2.37 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 140 time to evaluate : 0.308 Fit side-chains REVERT: F 80 ASP cc_start: 0.8468 (p0) cc_final: 0.7989 (p0) REVERT: A 94 MET cc_start: 0.8705 (ptm) cc_final: 0.8439 (ttp) REVERT: B 50 TYR cc_start: 0.8148 (t80) cc_final: 0.7798 (t80) outliers start: 11 outliers final: 4 residues processed: 144 average time/residue: 0.1038 time to fit residues: 20.3495 Evaluate side-chains 135 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 131 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain B residue 275 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 17 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 23 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.136190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.095541 restraints weight = 11542.721| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.92 r_work: 0.2939 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9040 Z= 0.157 Angle : 0.621 8.942 12288 Z= 0.310 Chirality : 0.044 0.252 1415 Planarity : 0.003 0.041 1524 Dihedral : 4.878 52.215 1179 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.26 % Allowed : 11.01 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.27), residues: 1064 helix: 3.45 (0.30), residues: 270 sheet: 1.10 (0.30), residues: 309 loop : -1.61 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 238 TYR 0.019 0.001 TYR G 34 PHE 0.015 0.001 PHE Z 40 TRP 0.009 0.001 TRP A 182 HIS 0.004 0.001 HIS F 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 ( 9008) covalent geometry : angle 0.58679 / 0.30 (12206) SS BOND : bond 0.00493 / 0.26 ( 14) SS BOND : angle 1.35615 / 0.82 ( 28) hydrogen bonds : bond 0.04949 / 3.22 ( 416) hydrogen bonds : angle 4.10617 / 2.74 ( 1200) link_BETA1-4 : bond 0.00319 / 0.16 ( 7) link_BETA1-4 : angle 1.30393 / 0.80 ( 21) link_NAG-ASN : bond 0.00700 / 0.45 ( 11) link_NAG-ASN : angle 3.70630 / 2.32 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: F 80 ASP cc_start: 0.8617 (p0) cc_final: 0.8138 (p0) REVERT: A 94 MET cc_start: 0.8740 (ptm) cc_final: 0.8283 (ttp) REVERT: B 50 TYR cc_start: 0.8154 (t80) cc_final: 0.7863 (t80) REVERT: B 54 MET cc_start: 0.7909 (mmm) cc_final: 0.7668 (mmm) REVERT: B 84 ASN cc_start: 0.8864 (t0) cc_final: 0.8629 (t0) outliers start: 12 outliers final: 6 residues processed: 141 average time/residue: 0.0971 time to fit residues: 18.7129 Evaluate side-chains 148 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 142 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 85 LYS Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain B residue 275 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 28 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 71 optimal weight: 0.0070 chunk 66 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.137087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.096291 restraints weight = 11794.677| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.97 r_work: 0.2956 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9040 Z= 0.127 Angle : 0.596 8.771 12288 Z= 0.297 Chirality : 0.043 0.316 1415 Planarity : 0.003 0.038 1524 Dihedral : 4.744 52.075 1179 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.47 % Allowed : 12.26 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.27), residues: 1064 helix: 3.56 (0.30), residues: 270 sheet: 1.10 (0.30), residues: 309 loop : -1.61 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 101 TYR 0.020 0.001 TYR G 34 PHE 0.014 0.001 PHE Z 40 TRP 0.009 0.001 TRP A 182 HIS 0.008 0.001 HIS F 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 9008) covalent geometry : angle 0.56340 / 0.29 (12206) SS BOND : bond 0.00377 / 0.20 ( 14) SS BOND : angle 1.25749 / 0.76 ( 28) hydrogen bonds : bond 0.04573 / 2.98 ( 416) hydrogen bonds : angle 3.98510 / 2.66 ( 1200) link_BETA1-4 : bond 0.00460 / 0.20 ( 7) link_BETA1-4 : angle 1.39084 / 0.83 ( 21) link_NAG-ASN : bond 0.00550 / 0.29 ( 11) link_NAG-ASN : angle 3.52291 / 2.20 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 56 GLU cc_start: 0.6895 (tt0) cc_final: 0.6543 (tt0) REVERT: F 80 ASP cc_start: 0.8614 (p0) cc_final: 0.8123 (p0) REVERT: E 56 GLU cc_start: 0.8115 (tt0) cc_final: 0.7893 (tt0) REVERT: B 50 TYR cc_start: 0.8123 (t80) cc_final: 0.7839 (t80) REVERT: B 84 ASN cc_start: 0.8754 (t0) cc_final: 0.8538 (t0) outliers start: 14 outliers final: 7 residues processed: 142 average time/residue: 0.1035 time to fit residues: 20.0737 Evaluate side-chains 139 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 132 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 85 LYS Chi-restraints excluded: chain F residue 98 CYS Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 275 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 16 optimal weight: 0.9990 chunk 81 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 121 ASN G 23 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.137168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.096989 restraints weight = 11595.276| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.89 r_work: 0.2961 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9040 Z= 0.126 Angle : 0.587 8.568 12288 Z= 0.293 Chirality : 0.043 0.249 1415 Planarity : 0.003 0.037 1524 Dihedral : 4.672 52.833 1179 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.36 % Allowed : 13.94 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.27), residues: 1064 helix: 3.57 (0.30), residues: 270 sheet: 1.06 (0.31), residues: 303 loop : -1.51 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 101 TYR 0.020 0.001 TYR G 34 PHE 0.013 0.001 PHE Z 40 TRP 0.009 0.001 TRP A 182 HIS 0.008 0.001 HIS F 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 9008) covalent geometry : angle 0.55764 / 0.29 (12206) SS BOND : bond 0.00366 / 0.20 ( 14) SS BOND : angle 1.19200 / 0.72 ( 28) hydrogen bonds : bond 0.04445 / 2.90 ( 416) hydrogen bonds : angle 3.95464 / 2.64 ( 1200) link_BETA1-4 : bond 0.00341 / 0.17 ( 7) link_BETA1-4 : angle 1.19330 / 0.75 ( 21) link_NAG-ASN : bond 0.00468 / 0.22 ( 11) link_NAG-ASN : angle 3.33310 / 2.07 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 56 GLU cc_start: 0.7059 (tt0) cc_final: 0.6711 (tt0) REVERT: F 80 ASP cc_start: 0.8684 (p0) cc_final: 0.8213 (p0) REVERT: F 123 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7362 (ppp) REVERT: G 47 ASP cc_start: 0.8534 (t0) cc_final: 0.8051 (t0) REVERT: G 53 ILE cc_start: 0.8282 (mm) cc_final: 0.7868 (mm) REVERT: E 56 GLU cc_start: 0.8161 (tt0) cc_final: 0.7924 (tt0) REVERT: B 50 TYR cc_start: 0.8144 (t80) cc_final: 0.7900 (t80) REVERT: B 54 MET cc_start: 0.7749 (mmm) cc_final: 0.7379 (mmm) REVERT: B 84 ASN cc_start: 0.8852 (t0) cc_final: 0.8638 (t0) outliers start: 13 outliers final: 7 residues processed: 143 average time/residue: 0.1027 time to fit residues: 20.1830 Evaluate side-chains 140 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 132 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 85 LYS Chi-restraints excluded: chain F residue 98 CYS Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 275 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 79 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 121 ASN A 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.134363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.093391 restraints weight = 11671.102| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.94 r_work: 0.2915 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9040 Z= 0.202 Angle : 0.640 8.577 12288 Z= 0.322 Chirality : 0.045 0.227 1415 Planarity : 0.003 0.042 1524 Dihedral : 4.918 55.268 1179 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.68 % Allowed : 14.36 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.27), residues: 1064 helix: 3.39 (0.30), residues: 270 sheet: 1.07 (0.31), residues: 309 loop : -1.68 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 101 TYR 0.021 0.001 TYR G 34 PHE 0.015 0.002 PHE D 22 TRP 0.010 0.001 TRP A 182 HIS 0.008 0.001 HIS F 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.20 ( 9008) covalent geometry : angle 0.61020 / 0.31 (12206) SS BOND : bond 0.00569 / 0.31 ( 14) SS BOND : angle 1.77686 / 1.17 ( 28) hydrogen bonds : bond 0.05233 / 3.42 ( 416) hydrogen bonds : angle 4.07236 / 2.73 ( 1200) link_BETA1-4 : bond 0.00297 / 0.13 ( 7) link_BETA1-4 : angle 1.22999 / 0.78 ( 21) link_NAG-ASN : bond 0.00393 / 0.18 ( 11) link_NAG-ASN : angle 3.32023 / 2.05 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 56 GLU cc_start: 0.6993 (tt0) cc_final: 0.6750 (tt0) REVERT: G 51 LYS cc_start: 0.7876 (mmmt) cc_final: 0.7157 (mtmt) REVERT: G 70 LYS cc_start: 0.8022 (mmtt) cc_final: 0.7097 (mppt) REVERT: B 50 TYR cc_start: 0.8088 (t80) cc_final: 0.7806 (t80) REVERT: B 54 MET cc_start: 0.7827 (mmm) cc_final: 0.7447 (mmm) REVERT: B 84 ASN cc_start: 0.8824 (t0) cc_final: 0.8617 (t0) outliers start: 16 outliers final: 10 residues processed: 141 average time/residue: 0.0961 time to fit residues: 18.5820 Evaluate side-chains 141 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 85 LYS Chi-restraints excluded: chain F residue 98 CYS Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 275 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 37 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.134369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.093617 restraints weight = 11747.348| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.94 r_work: 0.2917 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9040 Z= 0.188 Angle : 0.635 8.528 12288 Z= 0.319 Chirality : 0.044 0.229 1415 Planarity : 0.003 0.044 1524 Dihedral : 4.949 55.283 1179 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.78 % Allowed : 15.09 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.27), residues: 1064 helix: 3.35 (0.30), residues: 270 sheet: 1.08 (0.31), residues: 304 loop : -1.65 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 101 TYR 0.021 0.001 TYR G 34 PHE 0.013 0.001 PHE D 22 TRP 0.010 0.001 TRP A 182 HIS 0.007 0.001 HIS F 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.19 ( 9008) covalent geometry : angle 0.60735 / 0.31 (12206) SS BOND : bond 0.00487 / 0.26 ( 14) SS BOND : angle 1.55476 / 1.01 ( 28) hydrogen bonds : bond 0.05183 / 3.40 ( 416) hydrogen bonds : angle 4.06989 / 2.73 ( 1200) link_BETA1-4 : bond 0.00284 / 0.13 ( 7) link_BETA1-4 : angle 1.21635 / 0.76 ( 21) link_NAG-ASN : bond 0.00395 / 0.18 ( 11) link_NAG-ASN : angle 3.30012 / 2.04 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Y 52 ARG cc_start: 0.5837 (tpt-90) cc_final: 0.5594 (tpt90) REVERT: F 56 GLU cc_start: 0.7008 (tt0) cc_final: 0.6774 (tt0) REVERT: G 70 LYS cc_start: 0.8047 (mmtt) cc_final: 0.7288 (mppt) REVERT: A 248 ASN cc_start: 0.8801 (m-40) cc_final: 0.8580 (m-40) REVERT: B 50 TYR cc_start: 0.7993 (t80) cc_final: 0.7723 (t80) REVERT: B 54 MET cc_start: 0.7867 (mmm) cc_final: 0.7489 (mmm) outliers start: 17 outliers final: 12 residues processed: 148 average time/residue: 0.0986 time to fit residues: 19.9977 Evaluate side-chains 142 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 85 LYS Chi-restraints excluded: chain F residue 98 CYS Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 275 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 80 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 121 ASN G 23 GLN ** E 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.135867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.095961 restraints weight = 11676.032| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 3.07 r_work: 0.2942 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9040 Z= 0.135 Angle : 0.619 8.654 12288 Z= 0.310 Chirality : 0.043 0.238 1415 Planarity : 0.003 0.039 1524 Dihedral : 4.797 54.694 1179 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.78 % Allowed : 15.93 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.27), residues: 1064 helix: 3.45 (0.30), residues: 270 sheet: 1.17 (0.31), residues: 297 loop : -1.59 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 101 TYR 0.021 0.001 TYR G 34 PHE 0.011 0.001 PHE Z 40 TRP 0.009 0.001 TRP A 182 HIS 0.007 0.001 HIS F 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 9008) covalent geometry : angle 0.58916 / 0.30 (12206) SS BOND : bond 0.00389 / 0.22 ( 14) SS BOND : angle 1.21760 / 0.78 ( 28) hydrogen bonds : bond 0.04667 / 3.06 ( 416) hydrogen bonds : angle 3.95620 / 2.65 ( 1200) link_BETA1-4 : bond 0.00318 / 0.15 ( 7) link_BETA1-4 : angle 1.20631 / 0.75 ( 21) link_NAG-ASN : bond 0.00613 / 0.29 ( 11) link_NAG-ASN : angle 3.49009 / 2.18 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 56 GLU cc_start: 0.7043 (tt0) cc_final: 0.6839 (tt0) REVERT: G 47 ASP cc_start: 0.8608 (t0) cc_final: 0.8061 (t0) REVERT: G 51 LYS cc_start: 0.7827 (mmmt) cc_final: 0.7169 (mtmt) REVERT: G 70 LYS cc_start: 0.7981 (mmtt) cc_final: 0.7083 (mppt) REVERT: B 50 TYR cc_start: 0.7947 (t80) cc_final: 0.7703 (t80) REVERT: B 54 MET cc_start: 0.7864 (mmm) cc_final: 0.7507 (mmm) outliers start: 17 outliers final: 12 residues processed: 142 average time/residue: 0.0935 time to fit residues: 18.2779 Evaluate side-chains 147 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain F residue 85 LYS Chi-restraints excluded: chain F residue 98 CYS Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 275 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 12 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 121 ASN ** E 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.136335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.095707 restraints weight = 11637.587| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.94 r_work: 0.2951 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9040 Z= 0.135 Angle : 0.619 8.571 12288 Z= 0.310 Chirality : 0.043 0.238 1415 Planarity : 0.003 0.047 1524 Dihedral : 4.740 55.061 1179 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.57 % Allowed : 15.83 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.27), residues: 1064 helix: 3.48 (0.30), residues: 270 sheet: 1.18 (0.31), residues: 297 loop : -1.54 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Y 52 TYR 0.021 0.001 TYR G 34 PHE 0.011 0.001 PHE Z 40 TRP 0.009 0.001 TRP A 182 HIS 0.007 0.001 HIS F 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 ( 9008) covalent geometry : angle 0.59005 / 0.30 (12206) SS BOND : bond 0.00395 / 0.22 ( 14) SS BOND : angle 1.27448 / 0.80 ( 28) hydrogen bonds : bond 0.04556 / 2.98 ( 416) hydrogen bonds : angle 3.95031 / 2.65 ( 1200) link_BETA1-4 : bond 0.00333 / 0.16 ( 7) link_BETA1-4 : angle 1.18138 / 0.74 ( 21) link_NAG-ASN : bond 0.00521 / 0.25 ( 11) link_NAG-ASN : angle 3.39718 / 2.11 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 77 ASP cc_start: 0.8688 (t70) cc_final: 0.8451 (t70) REVERT: G 47 ASP cc_start: 0.8572 (t0) cc_final: 0.8001 (t0) REVERT: G 51 LYS cc_start: 0.7859 (mmmt) cc_final: 0.7186 (mtmt) REVERT: G 70 LYS cc_start: 0.7948 (mmtt) cc_final: 0.7039 (mppt) REVERT: A 248 ASN cc_start: 0.8697 (m-40) cc_final: 0.8424 (m-40) REVERT: B 50 TYR cc_start: 0.7923 (t80) cc_final: 0.7679 (t80) REVERT: B 54 MET cc_start: 0.7868 (mmm) cc_final: 0.7507 (mmm) outliers start: 15 outliers final: 13 residues processed: 145 average time/residue: 0.0863 time to fit residues: 16.9299 Evaluate side-chains 147 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain F residue 85 LYS Chi-restraints excluded: chain F residue 98 CYS Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 275 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 61 optimal weight: 0.8980 chunk 92 optimal weight: 0.0980 chunk 44 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 chunk 47 optimal weight: 0.1980 chunk 8 optimal weight: 2.9990 chunk 19 optimal weight: 0.4980 chunk 34 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 6 optimal weight: 0.3980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 121 ASN ** E 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.138967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.098995 restraints weight = 11580.453| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 3.08 r_work: 0.2994 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 9040 Z= 0.108 Angle : 0.597 8.625 12288 Z= 0.299 Chirality : 0.043 0.251 1415 Planarity : 0.003 0.048 1524 Dihedral : 4.544 54.266 1179 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.26 % Allowed : 16.46 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.27), residues: 1064 helix: 3.58 (0.30), residues: 270 sheet: 1.20 (0.31), residues: 298 loop : -1.48 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Y 52 TYR 0.022 0.001 TYR G 34 PHE 0.012 0.001 PHE Z 40 TRP 0.009 0.001 TRP A 182 HIS 0.008 0.001 HIS F 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 9008) covalent geometry : angle 0.57048 / 0.29 (12206) SS BOND : bond 0.00265 / 0.14 ( 14) SS BOND : angle 0.99403 / 0.62 ( 28) hydrogen bonds : bond 0.03891 / 2.54 ( 416) hydrogen bonds : angle 3.80865 / 2.55 ( 1200) link_BETA1-4 : bond 0.00374 / 0.18 ( 7) link_BETA1-4 : angle 1.16447 / 0.73 ( 21) link_NAG-ASN : bond 0.00584 / 0.28 ( 11) link_NAG-ASN : angle 3.28065 / 2.05 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 123 MET cc_start: 0.7950 (ppp) cc_final: 0.7484 (ppp) REVERT: G 47 ASP cc_start: 0.8458 (t0) cc_final: 0.7868 (t0) REVERT: G 51 LYS cc_start: 0.7786 (mmmt) cc_final: 0.7292 (mtmt) REVERT: B 50 TYR cc_start: 0.7863 (t80) cc_final: 0.7657 (t80) REVERT: B 54 MET cc_start: 0.7806 (mmm) cc_final: 0.7288 (mmm) outliers start: 12 outliers final: 10 residues processed: 148 average time/residue: 0.0857 time to fit residues: 17.4842 Evaluate side-chains 143 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain F residue 85 LYS Chi-restraints excluded: chain F residue 98 CYS Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain B residue 86 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 84 optimal weight: 5.9990 chunk 65 optimal weight: 0.0870 chunk 94 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 40 optimal weight: 0.1980 chunk 88 optimal weight: 0.0370 chunk 5 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.2640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 121 ASN ** E 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.136188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.096445 restraints weight = 11561.063| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.03 r_work: 0.2950 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 9040 Z= 0.156 Angle : 0.631 8.144 12288 Z= 0.319 Chirality : 0.044 0.233 1415 Planarity : 0.003 0.051 1524 Dihedral : 4.654 56.111 1179 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.17 % Favored : 94.74 % Rotamer: Outliers : 1.26 % Allowed : 16.77 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.27), residues: 1064 helix: 3.53 (0.30), residues: 270 sheet: 1.06 (0.31), residues: 304 loop : -1.47 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Y 52 TYR 0.025 0.001 TYR G 34 PHE 0.011 0.001 PHE Z 40 TRP 0.010 0.001 TRP A 182 HIS 0.007 0.001 HIS F 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 9008) covalent geometry : angle 0.60507 / 0.31 (12206) SS BOND : bond 0.00411 / 0.23 ( 14) SS BOND : angle 1.37305 / 0.88 ( 28) hydrogen bonds : bond 0.04526 / 2.96 ( 416) hydrogen bonds : angle 3.96943 / 2.68 ( 1200) link_BETA1-4 : bond 0.00315 / 0.15 ( 7) link_BETA1-4 : angle 1.18291 / 0.75 ( 21) link_NAG-ASN : bond 0.00447 / 0.21 ( 11) link_NAG-ASN : angle 3.24515 / 2.01 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2408.49 seconds wall clock time: 41 minutes 55.33 seconds (2515.33 seconds total)