Starting phenix.real_space_refine on Sun Jul 27 05:02:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8es7_28570/07_2025/8es7_28570.cif Found real_map, /net/cci-nas-00/data/ceres_data/8es7_28570/07_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_28570/07_2025/8es7_28570.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8es7_28570/07_2025/8es7_28570.map" model { file = "/net/cci-nas-00/data/ceres_data/8es7_28570/07_2025/8es7_28570.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8es7_28570/07_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-5711/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: 5.98, per 1000 atoms: 0.68 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: 2.69 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: 1.27 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: 2.58 Time building geometry restraints manager: 3.12 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: 1.680 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.810 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: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.160 ------------------------------------------------------------------------------- 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 : 0.791 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: 0.2108 time to fit residues: 47.8983 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 : 1.017 ------------------------------------------------------------------------------- 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: 0.8237 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 : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 56 GLU cc_start: 0.6846 (tt0) cc_final: 0.6586 (tt0) REVERT: F 80 ASP cc_start: 0.8411 (p0) cc_final: 0.7891 (p0) REVERT: F 101 ARG cc_start: 0.7518 (ttp80) cc_final: 0.7247 (ttm110) REVERT: E 56 GLU cc_start: 0.8217 (tt0) cc_final: 0.7998 (tt0) REVERT: E 104 LYS cc_start: 0.8304 (ttmt) cc_final: 0.7784 (tmmt) REVERT: A 94 MET cc_start: 0.8659 (ptm) cc_final: 0.8394 (ttp) REVERT: B 50 TYR cc_start: 0.8122 (t80) cc_final: 0.7721 (t80) outliers start: 7 outliers final: 2 residues processed: 148 average time/residue: 0.2179 time to fit residues: 43.9040 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 : 1.057 ------------------------------------------------------------------------------- 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: 0.9980 chunk 48 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3664 r_free = 0.3664 target = 0.138288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.098245 restraints weight = 11673.136| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 3.08 r_work: 0.2969 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9040 Z= 0.128 Angle : 0.626 8.738 12288 Z= 0.306 Chirality : 0.044 0.321 1415 Planarity : 0.003 0.037 1524 Dihedral : 10.109 69.496 1613 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.07 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: 1.01 (0.27), residues: 1064 helix: 3.54 (0.30), residues: 270 sheet: 1.20 (0.30), residues: 309 loop : -1.51 (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 0.019 0.001 TYR G 34 ARG 0.002 0.000 ARG A 238 Details of bonding type rmsd link_NAG-ASN : bond 0.00548 ( 11) link_NAG-ASN : angle 3.55729 ( 33) link_BETA1-4 : bond 0.00439 ( 7) link_BETA1-4 : angle 1.90170 ( 21) hydrogen bonds : bond 0.04504 ( 416) hydrogen bonds : angle 4.04098 ( 1200) SS BOND : bond 0.00389 ( 14) SS BOND : angle 1.72322 ( 28) covalent geometry : bond 0.00294 ( 9008) covalent geometry : angle 0.58904 (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 141 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 1.884 Fit side-chains revert: symmetry clash REVERT: F 80 ASP cc_start: 0.8568 (p0) cc_final: 0.8105 (p0) REVERT: F 101 ARG cc_start: 0.7549 (ttp80) cc_final: 0.7303 (ttm110) REVERT: G 47 ASP cc_start: 0.8463 (t0) cc_final: 0.8045 (t0) REVERT: G 51 LYS cc_start: 0.7654 (mmmt) cc_final: 0.7078 (mtmt) REVERT: E 56 GLU cc_start: 0.8196 (tt0) cc_final: 0.7990 (tt0) REVERT: A 94 MET cc_start: 0.8690 (ptm) cc_final: 0.8240 (ttp) REVERT: A 248 ASN cc_start: 0.8590 (m-40) cc_final: 0.8369 (m-40) REVERT: B 50 TYR cc_start: 0.8098 (t80) cc_final: 0.7799 (t80) REVERT: B 54 MET cc_start: 0.7781 (mmm) cc_final: 0.7550 (mmm) outliers start: 9 outliers final: 5 residues processed: 134 average time/residue: 0.2299 time to fit residues: 42.6916 Evaluate side-chains 132 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 127 time to evaluate : 1.040 ------------------------------------------------------------------------------- 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: 10.0000 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3661 r_free = 0.3661 target = 0.137969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.097940 restraints weight = 11514.438| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 3.06 r_work: 0.2968 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1157 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= 0.124 Angle : 0.613 9.031 12288 Z= 0.299 Chirality : 0.044 0.337 1415 Planarity : 0.003 0.037 1524 Dihedral : 8.579 62.059 1613 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.68 % Allowed : 11.01 % Favored : 87.32 % 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: 1.03 (0.27), residues: 1064 helix: 3.61 (0.30), residues: 270 sheet: 1.19 (0.30), residues: 309 loop : -1.51 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 182 HIS 0.008 0.001 HIS F 81 PHE 0.015 0.001 PHE Z 40 TYR 0.019 0.001 TYR G 34 ARG 0.002 0.000 ARG A 238 Details of bonding type rmsd link_NAG-ASN : bond 0.00438 ( 11) link_NAG-ASN : angle 3.67345 ( 33) link_BETA1-4 : bond 0.00447 ( 7) link_BETA1-4 : angle 1.95413 ( 21) hydrogen bonds : bond 0.04364 ( 416) hydrogen bonds : angle 3.93734 ( 1200) SS BOND : bond 0.00376 ( 14) SS BOND : angle 1.71348 ( 28) covalent geometry : bond 0.00285 ( 9008) covalent geometry : angle 0.57316 (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 152 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 56 GLU cc_start: 0.6772 (tt0) cc_final: 0.6480 (tt0) REVERT: F 80 ASP cc_start: 0.8564 (p0) cc_final: 0.8117 (p0) REVERT: G 47 ASP cc_start: 0.8463 (t0) cc_final: 0.7978 (t0) REVERT: G 53 ILE cc_start: 0.8158 (mm) cc_final: 0.7733 (mm) REVERT: A 248 ASN cc_start: 0.8602 (m-40) cc_final: 0.8374 (m-40) REVERT: B 50 TYR cc_start: 0.8123 (t80) cc_final: 0.7842 (t80) outliers start: 16 outliers final: 8 residues processed: 143 average time/residue: 0.2474 time to fit residues: 48.2124 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 : 1.072 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 33 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 10 optimal weight: 0.3980 chunk 65 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 62 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3670 r_free = 0.3670 target = 0.138640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.098612 restraints weight = 11505.659| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 3.07 r_work: 0.2978 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9040 Z= 0.114 Angle : 0.603 9.160 12288 Z= 0.294 Chirality : 0.043 0.351 1415 Planarity : 0.003 0.035 1524 Dihedral : 7.773 59.113 1613 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.57 % Allowed : 13.31 % 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: 1.08 (0.27), residues: 1064 helix: 3.67 (0.30), residues: 270 sheet: 1.22 (0.31), residues: 299 loop : -1.43 (0.27), residues: 495 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 0.014 0.001 PHE Z 40 TYR 0.020 0.001 TYR G 34 ARG 0.004 0.000 ARG E 101 Details of bonding type rmsd link_NAG-ASN : bond 0.00621 ( 11) link_NAG-ASN : angle 3.49633 ( 33) link_BETA1-4 : bond 0.00474 ( 7) link_BETA1-4 : angle 1.92142 ( 21) hydrogen bonds : bond 0.04152 ( 416) hydrogen bonds : angle 3.84427 ( 1200) SS BOND : bond 0.00336 ( 14) SS BOND : angle 1.40209 ( 28) covalent geometry : bond 0.00257 ( 9008) covalent geometry : angle 0.56799 (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 153 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 56 GLU cc_start: 0.6895 (tt0) cc_final: 0.6526 (tt0) REVERT: F 80 ASP cc_start: 0.8564 (p0) cc_final: 0.8101 (p0) REVERT: G 47 ASP cc_start: 0.8446 (t0) cc_final: 0.7851 (t0) REVERT: G 51 LYS cc_start: 0.7649 (mmmt) cc_final: 0.7151 (mtmt) REVERT: B 50 TYR cc_start: 0.8087 (t80) cc_final: 0.7848 (t80) outliers start: 15 outliers final: 9 residues processed: 145 average time/residue: 0.2190 time to fit residues: 43.5809 Evaluate side-chains 140 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 58 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 47 optimal weight: 0.6980 chunk 51 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 94 optimal weight: 4.9990 chunk 98 optimal weight: 0.3980 chunk 7 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 121 ASN A 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.137469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.096909 restraints weight = 11521.109| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.93 r_work: 0.2964 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9040 Z= 0.140 Angle : 0.619 9.178 12288 Z= 0.303 Chirality : 0.044 0.351 1415 Planarity : 0.003 0.037 1524 Dihedral : 7.419 57.008 1613 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.47 % Allowed : 14.68 % Favored : 83.86 % 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: 1.04 (0.27), residues: 1064 helix: 3.61 (0.30), residues: 270 sheet: 1.20 (0.31), residues: 309 loop : -1.51 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 182 HIS 0.006 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 0.00440 ( 11) link_NAG-ASN : angle 3.47732 ( 33) link_BETA1-4 : bond 0.00415 ( 7) link_BETA1-4 : angle 1.88880 ( 21) hydrogen bonds : bond 0.04461 ( 416) hydrogen bonds : angle 3.90140 ( 1200) SS BOND : bond 0.00401 ( 14) SS BOND : angle 1.59069 ( 28) covalent geometry : bond 0.00329 ( 9008) covalent geometry : angle 0.58354 (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 146 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 1.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 56 GLU cc_start: 0.7044 (tt0) cc_final: 0.6711 (tt0) REVERT: F 119 CYS cc_start: 0.5604 (m) cc_final: 0.5351 (m) REVERT: F 121 ASN cc_start: 0.5252 (OUTLIER) cc_final: 0.4988 (p0) REVERT: G 47 ASP cc_start: 0.8551 (t0) cc_final: 0.7935 (t0) REVERT: G 51 LYS cc_start: 0.7802 (mmmt) cc_final: 0.7068 (mtmt) REVERT: G 70 LYS cc_start: 0.8092 (mmtt) cc_final: 0.7095 (mppt) REVERT: B 50 TYR cc_start: 0.8068 (t80) cc_final: 0.7819 (t80) outliers start: 14 outliers final: 9 residues processed: 139 average time/residue: 0.3006 time to fit residues: 56.2144 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 : 0.974 ------------------------------------------------------------------------------- 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 121 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 81 optimal weight: 8.9990 chunk 96 optimal weight: 0.0040 chunk 93 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.7796 ------------------------------------------------------------------------------- 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 ** 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 = 0.3664 r_free = 0.3664 target = 0.138112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.098466 restraints weight = 11722.719| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 3.06 r_work: 0.2974 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9040 Z= 0.120 Angle : 0.617 9.331 12288 Z= 0.301 Chirality : 0.043 0.362 1415 Planarity : 0.003 0.036 1524 Dihedral : 7.116 55.741 1613 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.36 % Allowed : 15.30 % 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: 3.68 (0.29), residues: 270 sheet: 1.21 (0.31), residues: 303 loop : -1.49 (0.27), 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 0.012 0.001 PHE Z 40 TYR 0.020 0.001 TYR G 34 ARG 0.003 0.000 ARG E 101 Details of bonding type rmsd link_NAG-ASN : bond 0.00552 ( 11) link_NAG-ASN : angle 3.70940 ( 33) link_BETA1-4 : bond 0.00492 ( 7) link_BETA1-4 : angle 1.92344 ( 21) hydrogen bonds : bond 0.04255 ( 416) hydrogen bonds : angle 3.84543 ( 1200) SS BOND : bond 0.00358 ( 14) SS BOND : angle 1.57123 ( 28) covalent geometry : bond 0.00274 ( 9008) covalent geometry : angle 0.57771 (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 143 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 52 ARG cc_start: 0.6039 (tpt-90) cc_final: 0.5061 (tpt-90) REVERT: F 56 GLU cc_start: 0.6811 (tt0) cc_final: 0.6175 (tt0) REVERT: F 101 ARG cc_start: 0.7604 (ttp80) cc_final: 0.7101 (ttp-110) REVERT: G 47 ASP cc_start: 0.8464 (t0) cc_final: 0.7841 (t0) REVERT: G 70 LYS cc_start: 0.8075 (mmtt) cc_final: 0.7292 (mppt) REVERT: B 50 TYR cc_start: 0.8020 (t80) cc_final: 0.7790 (t80) outliers start: 13 outliers final: 9 residues processed: 136 average time/residue: 0.2224 time to fit residues: 41.6911 Evaluate side-chains 138 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 1.063 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 3 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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** ** A 248 ASN ** 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 = 0.3664 r_free = 0.3664 target = 0.138127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.098258 restraints weight = 11672.947| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 3.05 r_work: 0.2967 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9040 Z= 0.123 Angle : 0.622 9.400 12288 Z= 0.304 Chirality : 0.043 0.370 1415 Planarity : 0.003 0.048 1524 Dihedral : 6.766 53.847 1613 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.79 % Favored : 95.11 % Rotamer: Outliers : 1.47 % Allowed : 14.99 % 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: 1.02 (0.27), residues: 1064 helix: 3.64 (0.29), residues: 270 sheet: 1.14 (0.31), residues: 308 loop : -1.50 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 182 HIS 0.006 0.001 HIS F 81 PHE 0.012 0.001 PHE Z 40 TYR 0.021 0.001 TYR G 34 ARG 0.005 0.000 ARG E 101 Details of bonding type rmsd link_NAG-ASN : bond 0.00540 ( 11) link_NAG-ASN : angle 3.63288 ( 33) link_BETA1-4 : bond 0.00423 ( 7) link_BETA1-4 : angle 1.91673 ( 21) hydrogen bonds : bond 0.04245 ( 416) hydrogen bonds : angle 3.82074 ( 1200) SS BOND : bond 0.00380 ( 14) SS BOND : angle 1.46883 ( 28) covalent geometry : bond 0.00283 ( 9008) covalent geometry : angle 0.58574 (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 151 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 52 ARG cc_start: 0.6189 (tpt-90) cc_final: 0.5310 (tpt-90) REVERT: F 56 GLU cc_start: 0.6808 (tt0) cc_final: 0.6547 (tt0) REVERT: G 47 ASP cc_start: 0.8469 (t0) cc_final: 0.7925 (t0) REVERT: G 51 LYS cc_start: 0.7644 (mmmt) cc_final: 0.7130 (mtmt) REVERT: G 70 LYS cc_start: 0.8020 (mmtt) cc_final: 0.7097 (mppt) REVERT: B 50 TYR cc_start: 0.7988 (t80) cc_final: 0.7778 (t80) outliers start: 14 outliers final: 10 residues processed: 143 average time/residue: 0.2628 time to fit residues: 52.0478 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 : 1.325 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 0.8980 chunk 69 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 80 optimal weight: 7.9990 chunk 71 optimal weight: 0.0010 chunk 45 optimal weight: 2.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- 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** ** A 248 ASN ** 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 = 0.3671 r_free = 0.3671 target = 0.138613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.099465 restraints weight = 11529.637| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 3.00 r_work: 0.2977 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9040 Z= 0.118 Angle : 0.626 9.478 12288 Z= 0.307 Chirality : 0.043 0.377 1415 Planarity : 0.003 0.051 1524 Dihedral : 6.548 52.768 1613 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.79 % Favored : 95.11 % Rotamer: Outliers : 1.47 % Allowed : 15.09 % Favored : 83.44 % 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: 3.65 (0.29), residues: 270 sheet: 1.19 (0.32), residues: 294 loop : -1.41 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 182 HIS 0.006 0.001 HIS F 81 PHE 0.012 0.001 PHE Z 40 TYR 0.024 0.001 TYR G 34 ARG 0.003 0.000 ARG E 101 Details of bonding type rmsd link_NAG-ASN : bond 0.00522 ( 11) link_NAG-ASN : angle 3.59934 ( 33) link_BETA1-4 : bond 0.00373 ( 7) link_BETA1-4 : angle 1.89859 ( 21) hydrogen bonds : bond 0.04121 ( 416) hydrogen bonds : angle 3.82288 ( 1200) SS BOND : bond 0.00387 ( 14) SS BOND : angle 1.45712 ( 28) covalent geometry : bond 0.00269 ( 9008) covalent geometry : angle 0.59022 (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: 14 poor density : 133 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 52 ARG cc_start: 0.6168 (tpt-90) cc_final: 0.5915 (tpt90) REVERT: G 47 ASP cc_start: 0.8413 (t0) cc_final: 0.7840 (t0) REVERT: G 51 LYS cc_start: 0.7708 (mmmt) cc_final: 0.7189 (mtmt) REVERT: B 50 TYR cc_start: 0.7902 (t80) cc_final: 0.7702 (t80) outliers start: 14 outliers final: 9 residues processed: 140 average time/residue: 0.2917 time to fit residues: 56.7090 Evaluate side-chains 140 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 85 LYS Chi-restraints excluded: chain F residue 98 CYS Chi-restraints excluded: chain E residue 34 THR 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 83 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 81 optimal weight: 6.9990 chunk 14 optimal weight: 0.3980 chunk 68 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 93 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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** ** A 248 ASN ** 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 = 0.3674 r_free = 0.3674 target = 0.138855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.099573 restraints weight = 11599.990| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 3.00 r_work: 0.2990 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9040 Z= 0.116 Angle : 0.623 9.555 12288 Z= 0.307 Chirality : 0.044 0.380 1415 Planarity : 0.003 0.056 1524 Dihedral : 6.392 52.764 1613 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.70 % Favored : 95.21 % Rotamer: Outliers : 0.94 % Allowed : 15.72 % 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: 1.05 (0.27), residues: 1064 helix: 3.65 (0.29), residues: 270 sheet: 1.18 (0.32), residues: 294 loop : -1.41 (0.27), residues: 500 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 0.012 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 0.00501 ( 11) link_NAG-ASN : angle 3.58955 ( 33) link_BETA1-4 : bond 0.00340 ( 7) link_BETA1-4 : angle 1.88416 ( 21) hydrogen bonds : bond 0.04054 ( 416) hydrogen bonds : angle 3.82875 ( 1200) SS BOND : bond 0.00326 ( 14) SS BOND : angle 1.41243 ( 28) covalent geometry : bond 0.00268 ( 9008) covalent geometry : angle 0.58754 (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 145 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 136 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 52 ARG cc_start: 0.6097 (tpt-90) cc_final: 0.5876 (tpt90) REVERT: G 47 ASP cc_start: 0.8413 (t0) cc_final: 0.7840 (t0) REVERT: G 51 LYS cc_start: 0.7756 (mmmt) cc_final: 0.7238 (mtmt) REVERT: B 50 TYR cc_start: 0.7854 (t80) cc_final: 0.7652 (t80) outliers start: 9 outliers final: 8 residues processed: 141 average time/residue: 0.2131 time to fit residues: 41.5620 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 : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 85 LYS Chi-restraints excluded: chain F residue 98 CYS Chi-restraints excluded: chain E residue 34 THR 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: 0.6980 chunk 34 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 95 optimal weight: 0.6980 chunk 78 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 121 ASN ** E 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 ASN 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 = 0.138295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.098789 restraints weight = 11649.610| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 3.02 r_work: 0.2979 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1601 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= 0.124 Angle : 0.628 9.600 12288 Z= 0.311 Chirality : 0.044 0.380 1415 Planarity : 0.003 0.059 1524 Dihedral : 6.301 53.254 1613 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.26 % Allowed : 15.62 % 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 (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: 1.04 (0.27), residues: 1064 helix: 3.63 (0.29), residues: 270 sheet: 1.18 (0.32), residues: 294 loop : -1.41 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 182 HIS 0.006 0.001 HIS F 81 PHE 0.012 0.001 PHE Z 40 TYR 0.008 0.001 TYR A 50 ARG 0.003 0.000 ARG E 101 Details of bonding type rmsd link_NAG-ASN : bond 0.00482 ( 11) link_NAG-ASN : angle 3.56119 ( 33) link_BETA1-4 : bond 0.00331 ( 7) link_BETA1-4 : angle 1.83170 ( 21) hydrogen bonds : bond 0.04153 ( 416) hydrogen bonds : angle 3.82532 ( 1200) SS BOND : bond 0.00358 ( 14) SS BOND : angle 1.63804 ( 28) covalent geometry : bond 0.00291 ( 9008) covalent geometry : angle 0.59206 (12206) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4883.87 seconds wall clock time: 88 minutes 17.28 seconds (5297.28 seconds total)