Starting phenix.real_space_refine on Mon May 12 15:15:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8es7_28570/05_2025/8es7_28570.cif Found real_map, /net/cci-nas-00/data/ceres_data/8es7_28570/05_2025/8es7_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_28570/05_2025/8es7_28570.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8es7_28570/05_2025/8es7_28570.map" model { file = "/net/cci-nas-00/data/ceres_data/8es7_28570/05_2025/8es7_28570.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8es7_28570/05_2025/8es7_28570.cif" } resolution = 3.04 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= -0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.55, per 1000 atoms: 0.63 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: 2.61 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.19 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: 2.83 Time building geometry restraints manager: 2.97 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 - 21.95: 5222 21.95 - 43.90: 350 43.90 - 65.84: 71 65.84 - 87.79: 24 87.79 - 109.74: 17 Dihedral angle restraints: 5684 sinusoidal: 2545 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 5681 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: 0.000 Normalize map: mean=0, sd=1: 1.520 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: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.870 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 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 : 16.728 109.738 3628 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 (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: 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 TRP 0.031 0.001 TRP A 256 HIS 0.004 0.001 HIS F 61 PHE 0.018 0.001 PHE G 135 TYR 0.025 0.001 TYR G 34 ARG 0.006 0.000 ARG Y 52 Details of bonding type rmsd link_NAG-ASN : bond 0.00690 ( 11) link_NAG-ASN : angle 4.01699 ( 33) link_BETA1-4 : bond 0.00277 ( 7) link_BETA1-4 : angle 1.23746 ( 21) hydrogen bonds : bond 0.12180 ( 416) hydrogen bonds : angle 5.08934 ( 1200) SS BOND : bond 0.00361 ( 14) SS BOND : angle 1.67730 ( 28) covalent geometry : bond 0.00421 ( 9008) covalent geometry : angle 0.68131 (12206) *********************** 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 : 0.909 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: 0.1984 time to fit residues: 45.0761 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 : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.1980 chunk 78 optimal weight: 9.9990 chunk 43 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 60 optimal weight: 0.0870 chunk 94 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.138925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.099112 restraints weight = 11459.540| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 3.07 r_work: 0.2988 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.0840 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= 0.119 Angle : 0.630 8.685 12288 Z= 0.311 Chirality : 0.044 0.299 1415 Planarity : 0.003 0.037 1524 Dihedral : 11.646 82.556 1613 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.73 % Allowed : 7.86 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.96 (0.27), residues: 1064 helix: 3.49 (0.30), residues: 270 sheet: 1.14 (0.31), residues: 303 loop : -1.47 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 182 HIS 0.002 0.001 HIS E 61 PHE 0.018 0.001 PHE Z 40 TYR 0.013 0.001 TYR A 37 ARG 0.004 0.000 ARG E 101 Details of bonding type rmsd link_NAG-ASN : bond 0.00559 ( 11) link_NAG-ASN : angle 3.78664 ( 33) link_BETA1-4 : bond 0.00346 ( 7) link_BETA1-4 : angle 1.96632 ( 21) hydrogen bonds : bond 0.04554 ( 416) hydrogen bonds : angle 4.18466 ( 1200) SS BOND : bond 0.00512 ( 14) SS BOND : angle 1.11308 ( 28) covalent geometry : bond 0.00255 ( 9008) covalent geometry : angle 0.59224 (12206) *********************** 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 152 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 145 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 56 GLU cc_start: 0.6841 (tt0) cc_final: 0.6579 (tt0) REVERT: F 80 ASP cc_start: 0.8411 (p0) cc_final: 0.7891 (p0) REVERT: F 101 ARG cc_start: 0.7515 (ttp80) cc_final: 0.7243 (ttm110) REVERT: E 56 GLU cc_start: 0.8215 (tt0) cc_final: 0.7998 (tt0) REVERT: E 104 LYS cc_start: 0.8305 (ttmt) cc_final: 0.7785 (tmmt) REVERT: A 94 MET cc_start: 0.8652 (ptm) cc_final: 0.8386 (ttp) REVERT: B 50 TYR cc_start: 0.8121 (t80) cc_final: 0.7721 (t80) outliers start: 7 outliers final: 2 residues processed: 148 average time/residue: 0.2215 time to fit residues: 44.6862 Evaluate side-chains 132 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 130 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 90 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.138429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.097705 restraints weight = 11663.887| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.95 r_work: 0.2988 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1038 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= 0.123 Angle : 0.623 8.778 12288 Z= 0.304 Chirality : 0.044 0.324 1415 Planarity : 0.003 0.037 1524 Dihedral : 9.954 68.798 1613 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.94 % Allowed : 10.38 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.02 (0.27), residues: 1064 helix: 3.56 (0.30), residues: 270 sheet: 1.20 (0.30), residues: 309 loop : -1.50 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 182 HIS 0.009 0.001 HIS F 81 PHE 0.015 0.001 PHE Z 40 TYR 0.018 0.001 TYR G 34 ARG 0.002 0.000 ARG A 238 Details of bonding type rmsd link_NAG-ASN : bond 0.00506 ( 11) link_NAG-ASN : angle 3.53713 ( 33) link_BETA1-4 : bond 0.00450 ( 7) link_BETA1-4 : angle 1.87858 ( 21) hydrogen bonds : bond 0.04440 ( 416) hydrogen bonds : angle 4.02197 ( 1200) SS BOND : bond 0.00383 ( 14) SS BOND : angle 1.68588 ( 28) covalent geometry : bond 0.00280 ( 9008) covalent geometry : angle 0.58651 (12206) *********************** 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 143 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 134 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: F 80 ASP cc_start: 0.8631 (p0) cc_final: 0.8175 (p0) REVERT: F 101 ARG cc_start: 0.7546 (ttp80) cc_final: 0.7300 (ttm110) REVERT: G 47 ASP cc_start: 0.8535 (t0) cc_final: 0.8095 (t0) REVERT: G 51 LYS cc_start: 0.7690 (mmmt) cc_final: 0.7138 (mtmt) REVERT: G 53 ILE cc_start: 0.8258 (mm) cc_final: 0.7864 (mm) REVERT: E 56 GLU cc_start: 0.8270 (tt0) cc_final: 0.8070 (tt0) REVERT: A 94 MET cc_start: 0.8701 (ptm) cc_final: 0.8264 (ttp) REVERT: A 248 ASN cc_start: 0.8686 (m-40) cc_final: 0.8484 (m-40) REVERT: B 50 TYR cc_start: 0.8146 (t80) cc_final: 0.7844 (t80) REVERT: B 54 MET cc_start: 0.7855 (mmm) cc_final: 0.7604 (mmm) outliers start: 9 outliers final: 5 residues processed: 136 average time/residue: 0.2300 time to fit residues: 43.0705 Evaluate side-chains 134 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 129 time to evaluate : 1.057 ------------------------------------------------------------------------------- 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 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 81 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3640 r_free = 0.3640 target = 0.136118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.095257 restraints weight = 11553.006| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.93 r_work: 0.2941 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 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 : 0.004 0.042 9040 Z= 0.158 Angle : 0.636 8.976 12288 Z= 0.312 Chirality : 0.044 0.327 1415 Planarity : 0.003 0.040 1524 Dihedral : 8.647 62.155 1613 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.78 % Allowed : 11.43 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.95 (0.27), residues: 1064 helix: 3.53 (0.30), residues: 270 sheet: 1.16 (0.30), residues: 309 loop : -1.56 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 182 HIS 0.007 0.001 HIS F 81 PHE 0.015 0.001 PHE D 22 TYR 0.019 0.001 TYR G 34 ARG 0.002 0.000 ARG B 68 Details of bonding type rmsd link_NAG-ASN : bond 0.00558 ( 11) link_NAG-ASN : angle 3.66501 ( 33) link_BETA1-4 : bond 0.00448 ( 7) link_BETA1-4 : angle 1.92409 ( 21) hydrogen bonds : bond 0.04789 ( 416) hydrogen bonds : angle 4.01548 ( 1200) SS BOND : bond 0.00433 ( 14) SS BOND : angle 1.73237 ( 28) covalent geometry : bond 0.00376 ( 9008) covalent geometry : angle 0.59846 (12206) *********************** 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 151 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 56 GLU cc_start: 0.6823 (tt0) cc_final: 0.6561 (tt0) REVERT: F 80 ASP cc_start: 0.8656 (p0) cc_final: 0.8190 (p0) REVERT: G 70 LYS cc_start: 0.8154 (mmtt) cc_final: 0.7347 (mppt) REVERT: B 50 TYR cc_start: 0.8144 (t80) cc_final: 0.7850 (t80) REVERT: B 107 ASN cc_start: 0.8355 (m110) cc_final: 0.8049 (t0) outliers start: 17 outliers final: 9 residues processed: 141 average time/residue: 0.2262 time to fit residues: 43.2087 Evaluate side-chains 139 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 130 time to evaluate : 0.932 ------------------------------------------------------------------------------- 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 41 SER 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 72 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 10 optimal weight: 0.4980 chunk 65 optimal weight: 0.2980 chunk 60 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 62 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3666 r_free = 0.3666 target = 0.138285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.098307 restraints weight = 11507.228| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 3.08 r_work: 0.2978 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9040 Z= 0.111 Angle : 0.605 9.243 12288 Z= 0.295 Chirality : 0.043 0.354 1415 Planarity : 0.003 0.036 1524 Dihedral : 7.789 58.917 1613 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.47 % Allowed : 13.42 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.06 (0.27), residues: 1064 helix: 3.70 (0.30), residues: 270 sheet: 1.15 (0.31), residues: 303 loop : -1.45 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 182 HIS 0.007 0.001 HIS F 81 PHE 0.013 0.001 PHE Z 40 TYR 0.020 0.001 TYR G 34 ARG 0.005 0.000 ARG E 101 Details of bonding type rmsd link_NAG-ASN : bond 0.00569 ( 11) link_NAG-ASN : angle 3.53230 ( 33) link_BETA1-4 : bond 0.00432 ( 7) link_BETA1-4 : angle 1.92943 ( 21) hydrogen bonds : bond 0.04206 ( 416) hydrogen bonds : angle 3.88235 ( 1200) SS BOND : bond 0.00333 ( 14) SS BOND : angle 1.51291 ( 28) covalent geometry : bond 0.00247 ( 9008) covalent geometry : angle 0.56856 (12206) *********************** 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 157 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 56 GLU cc_start: 0.6927 (tt0) cc_final: 0.6714 (tt0) REVERT: F 80 ASP cc_start: 0.8569 (p0) cc_final: 0.8103 (p0) REVERT: F 119 CYS cc_start: 0.5752 (m) cc_final: 0.5466 (m) REVERT: G 47 ASP cc_start: 0.8447 (t0) cc_final: 0.7867 (t0) REVERT: G 51 LYS cc_start: 0.7645 (mmmt) cc_final: 0.7046 (mtmt) REVERT: G 70 LYS cc_start: 0.8067 (mmtt) cc_final: 0.7121 (mppt) REVERT: B 50 TYR cc_start: 0.8065 (t80) cc_final: 0.7844 (t80) REVERT: B 107 ASN cc_start: 0.8232 (m110) cc_final: 0.8027 (t0) outliers start: 14 outliers final: 7 residues processed: 151 average time/residue: 0.2247 time to fit residues: 46.2059 Evaluate side-chains 140 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 133 time to evaluate : 1.029 ------------------------------------------------------------------------------- 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 E residue 34 THR Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain B residue 86 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 58 optimal weight: 8.9990 chunk 4 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 47 optimal weight: 0.2980 chunk 51 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 98 optimal weight: 0.3980 chunk 7 optimal weight: 3.9990 chunk 6 optimal weight: 0.2980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.138936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.099934 restraints weight = 11426.049| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.97 r_work: 0.2993 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9040 Z= 0.108 Angle : 0.598 9.239 12288 Z= 0.292 Chirality : 0.043 0.362 1415 Planarity : 0.003 0.035 1524 Dihedral : 7.290 56.788 1613 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.15 % Allowed : 14.88 % 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 (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: 1.09 (0.27), residues: 1064 helix: 3.68 (0.30), residues: 270 sheet: 1.24 (0.31), residues: 297 loop : -1.43 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 182 HIS 0.007 0.001 HIS F 81 PHE 0.012 0.001 PHE Z 40 TYR 0.020 0.001 TYR G 34 ARG 0.005 0.000 ARG E 101 Details of bonding type rmsd link_NAG-ASN : bond 0.00464 ( 11) link_NAG-ASN : angle 3.43260 ( 33) link_BETA1-4 : bond 0.00433 ( 7) link_BETA1-4 : angle 1.93209 ( 21) hydrogen bonds : bond 0.04055 ( 416) hydrogen bonds : angle 3.82528 ( 1200) SS BOND : bond 0.00313 ( 14) SS BOND : angle 1.44043 ( 28) covalent geometry : bond 0.00239 ( 9008) covalent geometry : angle 0.56318 (12206) *********************** 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 143 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Y 52 ARG cc_start: 0.6032 (tpt-90) cc_final: 0.5033 (tpt-90) REVERT: F 56 GLU cc_start: 0.6877 (tt0) cc_final: 0.6519 (tt0) REVERT: F 119 CYS cc_start: 0.5695 (m) cc_final: 0.5070 (m) REVERT: G 47 ASP cc_start: 0.8462 (t0) cc_final: 0.7874 (t0) REVERT: G 51 LYS cc_start: 0.7738 (mmmt) cc_final: 0.7084 (mtmt) REVERT: G 70 LYS cc_start: 0.8054 (mmtt) cc_final: 0.7116 (mppt) REVERT: B 50 TYR cc_start: 0.8026 (t80) cc_final: 0.7784 (t80) outliers start: 11 outliers final: 7 residues processed: 138 average time/residue: 0.2176 time to fit residues: 41.3248 Evaluate side-chains 133 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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 E residue 34 THR Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain B residue 86 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 81 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3666 r_free = 0.3666 target = 0.138143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.098658 restraints weight = 11656.361| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 3.03 r_work: 0.2977 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9040 Z= 0.125 Angle : 0.625 9.266 12288 Z= 0.303 Chirality : 0.045 0.481 1415 Planarity : 0.003 0.037 1524 Dihedral : 7.130 55.247 1613 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.26 % Allowed : 15.20 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.06 (0.27), residues: 1064 helix: 3.64 (0.29), residues: 270 sheet: 1.19 (0.32), residues: 293 loop : -1.40 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 182 HIS 0.006 0.001 HIS F 81 PHE 0.011 0.001 PHE Z 40 TYR 0.020 0.001 TYR G 34 ARG 0.005 0.000 ARG E 101 Details of bonding type rmsd link_NAG-ASN : bond 0.00566 ( 11) link_NAG-ASN : angle 3.82648 ( 33) link_BETA1-4 : bond 0.00355 ( 7) link_BETA1-4 : angle 1.97195 ( 21) hydrogen bonds : bond 0.04233 ( 416) hydrogen bonds : angle 3.82225 ( 1200) SS BOND : bond 0.00373 ( 14) SS BOND : angle 1.52811 ( 28) covalent geometry : bond 0.00288 ( 9008) covalent geometry : angle 0.58405 (12206) *********************** 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 141 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 52 ARG cc_start: 0.6031 (tpt-90) cc_final: 0.5104 (tpt-90) REVERT: G 47 ASP cc_start: 0.8545 (t0) cc_final: 0.8003 (t0) REVERT: G 51 LYS cc_start: 0.7820 (mmmt) cc_final: 0.7114 (mtmt) REVERT: G 70 LYS cc_start: 0.8053 (mmtt) cc_final: 0.7057 (mppt) REVERT: B 50 TYR cc_start: 0.8051 (t80) cc_final: 0.7816 (t80) outliers start: 12 outliers final: 10 residues processed: 135 average time/residue: 0.2153 time to fit residues: 39.8789 Evaluate side-chains 137 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 3 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 40 optimal weight: 0.2980 chunk 95 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3639 r_free = 0.3639 target = 0.135783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.095992 restraints weight = 11724.076| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 3.05 r_work: 0.2933 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9040 Z= 0.165 Angle : 0.651 9.661 12288 Z= 0.321 Chirality : 0.045 0.367 1415 Planarity : 0.003 0.040 1524 Dihedral : 6.863 54.007 1613 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.47 % Allowed : 14.88 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.95 (0.27), residues: 1064 helix: 3.55 (0.29), residues: 270 sheet: 1.15 (0.31), residues: 303 loop : -1.54 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 182 HIS 0.006 0.001 HIS F 61 PHE 0.014 0.001 PHE D 22 TYR 0.021 0.001 TYR G 34 ARG 0.006 0.000 ARG E 101 Details of bonding type rmsd link_NAG-ASN : bond 0.00427 ( 11) link_NAG-ASN : angle 3.75142 ( 33) link_BETA1-4 : bond 0.00353 ( 7) link_BETA1-4 : angle 1.84164 ( 21) hydrogen bonds : bond 0.04822 ( 416) hydrogen bonds : angle 3.94296 ( 1200) SS BOND : bond 0.00483 ( 14) SS BOND : angle 1.66321 ( 28) covalent geometry : bond 0.00395 ( 9008) covalent geometry : angle 0.61334 (12206) *********************** 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 147 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 52 ARG cc_start: 0.6159 (tpt-90) cc_final: 0.5920 (tpt90) REVERT: F 119 CYS cc_start: 0.5784 (m) cc_final: 0.5527 (m) REVERT: G 47 ASP cc_start: 0.8495 (t0) cc_final: 0.7957 (t0) REVERT: G 53 ILE cc_start: 0.8207 (mm) cc_final: 0.7777 (mm) REVERT: G 70 LYS cc_start: 0.8091 (mmtt) cc_final: 0.7326 (mppt) REVERT: B 50 TYR cc_start: 0.7920 (t80) cc_final: 0.7693 (t80) REVERT: B 54 MET cc_start: 0.7724 (mmm) cc_final: 0.7371 (mmm) outliers start: 14 outliers final: 12 residues processed: 140 average time/residue: 0.2266 time to fit residues: 43.5060 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 : 1.013 ------------------------------------------------------------------------------- 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 23 GLN 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 2.9990 chunk 69 optimal weight: 0.0670 chunk 25 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 chunk 73 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 80 optimal weight: 9.9990 chunk 71 optimal weight: 0.1980 chunk 45 optimal weight: 4.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3677 r_free = 0.3677 target = 0.139117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.100077 restraints weight = 11526.091| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 3.00 r_work: 0.2994 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9040 Z= 0.107 Angle : 0.616 9.693 12288 Z= 0.303 Chirality : 0.043 0.388 1415 Planarity : 0.003 0.048 1524 Dihedral : 6.442 52.237 1613 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.70 % Favored : 95.21 % Rotamer: Outliers : 1.05 % Allowed : 15.62 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.06 (0.27), residues: 1064 helix: 3.71 (0.29), residues: 270 sheet: 1.07 (0.31), residues: 310 loop : -1.43 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 182 HIS 0.006 0.001 HIS F 81 PHE 0.011 0.001 PHE Z 40 TYR 0.022 0.001 TYR G 34 ARG 0.005 0.000 ARG E 101 Details of bonding type rmsd link_NAG-ASN : bond 0.00581 ( 11) link_NAG-ASN : angle 3.66361 ( 33) link_BETA1-4 : bond 0.00357 ( 7) link_BETA1-4 : angle 1.89029 ( 21) hydrogen bonds : bond 0.03959 ( 416) hydrogen bonds : angle 3.77925 ( 1200) SS BOND : bond 0.00299 ( 14) SS BOND : angle 1.40074 ( 28) covalent geometry : bond 0.00236 ( 9008) covalent geometry : angle 0.57915 (12206) *********************** 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 147 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 52 ARG cc_start: 0.6132 (tpt-90) cc_final: 0.5930 (tpt90) REVERT: F 119 CYS cc_start: 0.5598 (m) cc_final: 0.5370 (m) REVERT: G 47 ASP cc_start: 0.8430 (t0) cc_final: 0.7856 (t0) REVERT: G 51 LYS cc_start: 0.7713 (mmmt) cc_final: 0.7252 (mtmt) REVERT: B 50 TYR cc_start: 0.7878 (t80) cc_final: 0.7653 (t80) REVERT: B 54 MET cc_start: 0.7684 (mmm) cc_final: 0.7327 (mmm) outliers start: 10 outliers final: 7 residues processed: 142 average time/residue: 0.2145 time to fit residues: 41.7401 Evaluate side-chains 137 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 130 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 E residue 90 LEU Chi-restraints excluded: chain A residue 35 PHE 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 83 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 65 optimal weight: 0.0870 chunk 81 optimal weight: 10.0000 chunk 14 optimal weight: 0.0570 chunk 68 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 overall best weight: 0.9078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3665 r_free = 0.3665 target = 0.138094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.098718 restraints weight = 11648.727| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 3.03 r_work: 0.2969 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9040 Z= 0.128 Angle : 0.629 9.577 12288 Z= 0.310 Chirality : 0.044 0.381 1415 Planarity : 0.003 0.053 1524 Dihedral : 6.337 53.561 1613 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.98 % Favored : 94.92 % Rotamer: Outliers : 1.05 % Allowed : 15.72 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.02 (0.27), residues: 1064 helix: 3.62 (0.29), residues: 270 sheet: 1.06 (0.31), residues: 310 loop : -1.44 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 182 HIS 0.006 0.001 HIS F 81 PHE 0.011 0.001 PHE Z 40 TYR 0.009 0.001 TYR A 50 ARG 0.005 0.000 ARG E 101 Details of bonding type rmsd link_NAG-ASN : bond 0.00451 ( 11) link_NAG-ASN : angle 3.58825 ( 33) link_BETA1-4 : bond 0.00324 ( 7) link_BETA1-4 : angle 1.83132 ( 21) hydrogen bonds : bond 0.04239 ( 416) hydrogen bonds : angle 3.83357 ( 1200) SS BOND : bond 0.00382 ( 14) SS BOND : angle 1.59082 ( 28) covalent geometry : bond 0.00303 ( 9008) covalent geometry : angle 0.59295 (12206) ********************** 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 142 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 119 CYS cc_start: 0.5667 (m) cc_final: 0.5424 (m) REVERT: G 47 ASP cc_start: 0.8445 (t0) cc_final: 0.7877 (t0) REVERT: G 51 LYS cc_start: 0.7733 (mmmt) cc_final: 0.7194 (mtmt) REVERT: B 50 TYR cc_start: 0.7870 (t80) cc_final: 0.7639 (t80) REVERT: B 54 MET cc_start: 0.7718 (mmm) cc_final: 0.7350 (mmm) outliers start: 10 outliers final: 8 residues processed: 137 average time/residue: 0.2171 time to fit residues: 40.8451 Evaluate side-chains 138 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 99 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 95 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3637 r_free = 0.3637 target = 0.135583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.095278 restraints weight = 11715.538| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.92 r_work: 0.2940 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 9040 Z= 0.171 Angle : 0.662 9.925 12288 Z= 0.329 Chirality : 0.045 0.381 1415 Planarity : 0.003 0.056 1524 Dihedral : 6.419 54.741 1613 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.55 % Favored : 94.36 % Rotamer: Outliers : 1.15 % Allowed : 15.83 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.94 (0.27), residues: 1064 helix: 3.50 (0.30), residues: 270 sheet: 1.15 (0.31), residues: 303 loop : -1.52 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 182 HIS 0.006 0.001 HIS F 61 PHE 0.013 0.001 PHE D 22 TYR 0.012 0.001 TYR B 35 ARG 0.005 0.000 ARG Y 52 Details of bonding type rmsd link_NAG-ASN : bond 0.00405 ( 11) link_NAG-ASN : angle 3.64407 ( 33) link_BETA1-4 : bond 0.00300 ( 7) link_BETA1-4 : angle 1.76097 ( 21) hydrogen bonds : bond 0.04828 ( 416) hydrogen bonds : angle 3.98134 ( 1200) SS BOND : bond 0.00466 ( 14) SS BOND : angle 1.77836 ( 28) covalent geometry : bond 0.00413 ( 9008) covalent geometry : angle 0.62680 (12206) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5008.01 seconds wall clock time: 87 minutes 39.97 seconds (5259.97 seconds total)