Starting phenix.real_space_refine on Thu Sep 26 12:36:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kex_22842/09_2024/7kex_22842.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kex_22842/09_2024/7kex_22842.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kex_22842/09_2024/7kex_22842.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kex_22842/09_2024/7kex_22842.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kex_22842/09_2024/7kex_22842.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kex_22842/09_2024/7kex_22842.cif" } resolution = 4.25 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= -0.002 sd= 0.089 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 48 5.16 5 C 8181 2.51 5 N 2163 2.21 5 O 2517 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 12909 Number of models: 1 Model: "" Number of chains: 7 Chain: "G" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 923 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "A" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1716 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 11, 'TRANS': 208} Chain breaks: 1 Chain: "K" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 812 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "E" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 735 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "M" 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: "N" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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 Restraints were copied for chains: O, Q, J, L, C, B, P, R, I, H, D, F Time building chain proxies: 6.90, per 1000 atoms: 0.53 Number of scatterers: 12909 At special positions: 0 Unit cell: (136.85, 146.05, 118.45, 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 48 16.00 O 2517 8.00 N 2163 7.00 C 8181 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 511 " - pdb=" SG CYS D 556 " distance=2.04 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 ALPHA1-6 " BMA N 3 " - " MAN N 4 " " BMA P 3 " - " MAN P 4 " " BMA R 3 " - " MAN R 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " NAG-ASN " NAG A 401 " - " ASN A 228 " " NAG A 402 " - " ASN A 238 " " NAG B 401 " - " ASN B 228 " " NAG B 402 " - " ASN B 238 " " NAG C 401 " - " ASN C 228 " " NAG C 402 " - " ASN C 238 " " NAG M 1 " - " ASN A 257 " " NAG N 1 " - " ASN D 563 " " NAG O 1 " - " ASN B 257 " " NAG P 1 " - " ASN E 563 " " NAG Q 1 " - " ASN C 257 " " NAG R 1 " - " ASN F 563 " Time building additional restraints: 3.67 Conformation dependent library (CDL) restraints added in 1.6 seconds 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2934 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 33 sheets defined 20.0% alpha, 34.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.01 Creating SS restraints... Processing helix chain 'J' and resid 30 through 32 No H-bonds generated for 'chain 'J' and resid 30 through 32' Processing helix chain 'J' and resid 51 through 53 No H-bonds generated for 'chain 'J' and resid 51 through 53' Processing helix chain 'J' and resid 80 through 84 Processing helix chain 'G' and resid 62 through 65 Processing helix chain 'G' and resid 74 through 76 No H-bonds generated for 'chain 'G' and resid 74 through 76' Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'G' and resid 101 through 104 Processing helix chain 'A' and resid 59 through 63 Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 78 through 84 Processing helix chain 'A' and resid 249 through 264 Processing helix chain 'D' and resid 527 through 532 removed outlier: 4.305A pdb=" N ALA D 530 " --> pdb=" O ILE D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 541 Processing helix chain 'D' and resid 553 through 575 removed outlier: 4.316A pdb=" N GLN D 567 " --> pdb=" O ASN D 563 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA D 568 " --> pdb=" O GLU D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 598 removed outlier: 4.074A pdb=" N ARG D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) Processing helix chain 'K' and resid 30 through 32 No H-bonds generated for 'chain 'K' and resid 30 through 32' Processing helix chain 'K' and resid 51 through 53 No H-bonds generated for 'chain 'K' and resid 51 through 53' Processing helix chain 'K' and resid 80 through 84 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 101 through 104 Processing helix chain 'B' and resid 59 through 63 Processing helix chain 'B' and resid 71 through 74 Processing helix chain 'B' and resid 78 through 84 Processing helix chain 'B' and resid 249 through 264 Processing helix chain 'E' and resid 527 through 532 removed outlier: 4.304A pdb=" N ALA E 530 " --> pdb=" O ILE E 527 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 541 Processing helix chain 'E' and resid 553 through 575 removed outlier: 4.315A pdb=" N GLN E 567 " --> pdb=" O ASN E 563 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA E 568 " --> pdb=" O GLU E 564 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 598 removed outlier: 4.073A pdb=" N ARG E 596 " --> pdb=" O PHE E 592 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 51 through 53 No H-bonds generated for 'chain 'L' and resid 51 through 53' Processing helix chain 'L' and resid 80 through 84 Processing helix chain 'I' and resid 62 through 65 Processing helix chain 'I' and resid 74 through 76 No H-bonds generated for 'chain 'I' and resid 74 through 76' Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'I' and resid 101 through 104 Processing helix chain 'C' and resid 59 through 63 Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 78 through 84 Processing helix chain 'C' and resid 249 through 264 Processing helix chain 'F' and resid 527 through 532 removed outlier: 4.305A pdb=" N ALA F 530 " --> pdb=" O ILE F 527 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 541 Processing helix chain 'F' and resid 553 through 575 removed outlier: 4.316A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA F 568 " --> pdb=" O GLU F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 598 removed outlier: 4.074A pdb=" N ARG F 596 " --> pdb=" O PHE F 592 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.175A pdb=" N LEU J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N PHE J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N TYR J 50 " --> pdb=" O PHE J 34 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.175A pdb=" N LEU J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'G' and resid 10 through 12 Processing sheet with id=AA6, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.658A pdb=" N TYR G 34 " --> pdb=" O ARG G 50 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ARG G 50 " --> pdb=" O TYR G 34 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA G 40 " --> pdb=" O GLY G 44 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY G 44 " --> pdb=" O ALA G 40 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TYR G 60 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE A 274 " --> pdb=" O TYR G 60 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TYR A 241 " --> pdb=" O TRP A 275 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL A 277 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N GLN A 243 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N SER A 142 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLU A 112 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 35 through 38 removed outlier: 3.927A pdb=" N LEU A 35 " --> pdb=" O SER A 46 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 159 through 161 removed outlier: 5.656A pdb=" N ASN A 69 " --> pdb=" O GLU A 103 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AB1, first strand: chain 'A' and resid 96 through 97 removed outlier: 6.865A pdb=" N VAL A 96 " --> pdb=" O THR D 581 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 105 through 109 removed outlier: 6.644A pdb=" N GLU A 106 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N HIS A 139 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AB4, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.175A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N PHE K 34 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N TYR K 50 " --> pdb=" O PHE K 34 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.175A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB7, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AB8, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.658A pdb=" N TYR H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ARG H 50 " --> pdb=" O TYR H 34 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA H 40 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N TYR H 60 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE B 274 " --> pdb=" O TYR H 60 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N TYR B 241 " --> pdb=" O TRP B 275 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N VAL B 277 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N GLN B 243 " --> pdb=" O VAL B 277 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N SER B 142 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLU B 112 " --> pdb=" O GLY B 143 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 35 through 38 removed outlier: 3.927A pdb=" N LEU B 35 " --> pdb=" O SER B 46 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 159 through 161 removed outlier: 5.657A pdb=" N ASN B 69 " --> pdb=" O GLU B 103 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 86 through 89 Processing sheet with id=AC3, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.866A pdb=" N VAL B 96 " --> pdb=" O THR E 581 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 105 through 109 removed outlier: 6.644A pdb=" N GLU B 106 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N HIS B 139 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N CYS B 108 " --> pdb=" O HIS B 139 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.175A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N PHE L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N TYR L 50 " --> pdb=" O PHE L 34 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.175A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AC9, first strand: chain 'I' and resid 10 through 12 Processing sheet with id=AD1, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.659A pdb=" N TYR I 34 " --> pdb=" O ARG I 50 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ARG I 50 " --> pdb=" O TYR I 34 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA I 40 " --> pdb=" O GLY I 44 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N TYR I 60 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE C 274 " --> pdb=" O TYR I 60 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TYR C 241 " --> pdb=" O TRP C 275 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL C 277 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N GLN C 243 " --> pdb=" O VAL C 277 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR C 240 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N SER C 142 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLU C 112 " --> pdb=" O GLY C 143 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 35 through 38 removed outlier: 3.926A pdb=" N LEU C 35 " --> pdb=" O SER C 46 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 159 through 161 removed outlier: 5.657A pdb=" N ASN C 69 " --> pdb=" O GLU C 103 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 86 through 89 Processing sheet with id=AD5, first strand: chain 'C' and resid 96 through 97 removed outlier: 6.866A pdb=" N VAL C 96 " --> pdb=" O THR F 581 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'C' and resid 105 through 109 removed outlier: 6.645A pdb=" N GLU C 106 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N HIS C 139 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N CYS C 108 " --> pdb=" O HIS C 139 " (cutoff:3.500A) 495 hydrogen bonds defined for protein. 1179 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: 4.32 Time building geometry restraints manager: 4.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2316 1.31 - 1.45: 4144 1.45 - 1.58: 6590 1.58 - 1.72: 90 1.72 - 1.85: 60 Bond restraints: 13200 Sorted by residual: bond pdb=" CB PHE H 108 " pdb=" CG PHE H 108 " ideal model delta sigma weight residual 1.502 1.356 0.146 2.30e-02 1.89e+03 4.04e+01 bond pdb=" CB ILE B 185 " pdb=" CG1 ILE B 185 " ideal model delta sigma weight residual 1.530 1.657 -0.127 2.00e-02 2.50e+03 4.03e+01 bond pdb=" CB PHE G 108 " pdb=" CG PHE G 108 " ideal model delta sigma weight residual 1.502 1.356 0.146 2.30e-02 1.89e+03 4.02e+01 bond pdb=" CB PHE I 108 " pdb=" CG PHE I 108 " ideal model delta sigma weight residual 1.502 1.357 0.145 2.30e-02 1.89e+03 3.99e+01 bond pdb=" CB ILE C 185 " pdb=" CG1 ILE C 185 " ideal model delta sigma weight residual 1.530 1.656 -0.126 2.00e-02 2.50e+03 3.97e+01 ... (remaining 13195 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 14402 2.19 - 4.38: 2896 4.38 - 6.57: 529 6.57 - 8.76: 92 8.76 - 10.95: 15 Bond angle restraints: 17934 Sorted by residual: angle pdb=" C PRO B 93 " pdb=" N PRO B 94 " pdb=" CA PRO B 94 " ideal model delta sigma weight residual 120.31 127.77 -7.46 9.80e-01 1.04e+00 5.80e+01 angle pdb=" C PRO A 93 " pdb=" N PRO A 94 " pdb=" CA PRO A 94 " ideal model delta sigma weight residual 120.31 127.74 -7.43 9.80e-01 1.04e+00 5.75e+01 angle pdb=" C PRO C 93 " pdb=" N PRO C 94 " pdb=" CA PRO C 94 " ideal model delta sigma weight residual 120.31 127.70 -7.39 9.80e-01 1.04e+00 5.69e+01 angle pdb=" C GLY D 536 " pdb=" N PRO D 537 " pdb=" CA PRO D 537 " ideal model delta sigma weight residual 120.03 127.28 -7.25 9.90e-01 1.02e+00 5.37e+01 angle pdb=" C GLY E 536 " pdb=" N PRO E 537 " pdb=" CA PRO E 537 " ideal model delta sigma weight residual 120.03 127.28 -7.25 9.90e-01 1.02e+00 5.36e+01 ... (remaining 17929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.44: 7759 21.44 - 42.89: 167 42.89 - 64.33: 51 64.33 - 85.78: 60 85.78 - 107.22: 30 Dihedral angle restraints: 8067 sinusoidal: 3456 harmonic: 4611 Sorted by residual: dihedral pdb=" C3 BMA R 3 " pdb=" C4 BMA R 3 " pdb=" C5 BMA R 3 " pdb=" O5 BMA R 3 " ideal model delta sinusoidal sigma weight residual 47.62 -59.60 107.22 1 3.00e+01 1.11e-03 1.38e+01 dihedral pdb=" C3 BMA P 3 " pdb=" C4 BMA P 3 " pdb=" C5 BMA P 3 " pdb=" O5 BMA P 3 " ideal model delta sinusoidal sigma weight residual 47.62 -59.59 107.21 1 3.00e+01 1.11e-03 1.38e+01 dihedral pdb=" C3 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C5 BMA N 3 " pdb=" O5 BMA N 3 " ideal model delta sinusoidal sigma weight residual 47.62 -59.56 107.18 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 8064 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1347 0.095 - 0.189: 500 0.189 - 0.284: 144 0.284 - 0.379: 43 0.379 - 0.474: 36 Chirality restraints: 2070 Sorted by residual: chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.06e+02 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.06e+02 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.04e+02 ... (remaining 2067 not shown) Planarity restraints: 2274 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 228 " 0.055 2.00e-02 2.50e+03 5.68e-02 4.03e+01 pdb=" CG ASN C 228 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN C 228 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN C 228 " -0.087 2.00e-02 2.50e+03 pdb=" C1 NAG C 401 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 228 " -0.055 2.00e-02 2.50e+03 5.65e-02 4.00e+01 pdb=" CG ASN B 228 " 0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN B 228 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN B 228 " 0.087 2.00e-02 2.50e+03 pdb=" C1 NAG B 401 " -0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 228 " 0.054 2.00e-02 2.50e+03 5.64e-02 3.97e+01 pdb=" CG ASN A 228 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN A 228 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN A 228 " -0.087 2.00e-02 2.50e+03 pdb=" C1 NAG A 401 " 0.068 2.00e-02 2.50e+03 ... (remaining 2271 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 106 2.59 - 3.17: 11047 3.17 - 3.75: 20636 3.75 - 4.32: 30381 4.32 - 4.90: 46676 Nonbonded interactions: 108846 Sorted by model distance: nonbonded pdb=" SG CYS L 23 " pdb=" SG CYS L 89 " model vdw 2.018 3.760 nonbonded pdb=" SG CYS J 23 " pdb=" SG CYS J 89 " model vdw 2.018 3.760 nonbonded pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " model vdw 2.019 3.760 nonbonded pdb=" SG CYS K 23 " pdb=" SG CYS K 89 " model vdw 2.019 3.760 nonbonded pdb=" SG CYS G 22 " pdb=" SG CYS G 96 " model vdw 2.020 3.760 ... (remaining 108841 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 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'R' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.710 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 31.570 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 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 : 0.022 0.146 13200 Z= 1.397 Angle : 1.876 10.947 17934 Z= 1.227 Chirality : 0.123 0.474 2070 Planarity : 0.009 0.037 2262 Dihedral : 14.860 107.219 5130 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.57 % Allowed : 3.02 % Favored : 96.42 % Rotamer: Outliers : 0.22 % Allowed : 0.67 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.20), residues: 1590 helix: 0.25 (0.32), residues: 186 sheet: 0.24 (0.23), residues: 504 loop : 0.68 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.013 TRP D 531 HIS 0.030 0.005 HIS A 139 PHE 0.048 0.007 PHE B 132 TYR 0.062 0.010 TYR A 109 ARG 0.008 0.001 ARG J 46 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 336 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 71 ASP cc_start: 0.8402 (t0) cc_final: 0.8026 (p0) REVERT: J 76 ILE cc_start: 0.9104 (mt) cc_final: 0.8829 (tt) REVERT: G 43 GLN cc_start: 0.8999 (mt0) cc_final: 0.8764 (pt0) REVERT: G 48 MET cc_start: 0.9245 (mtp) cc_final: 0.8809 (mtp) REVERT: A 100 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8728 (tt0) REVERT: A 184 LEU cc_start: 0.8715 (mt) cc_final: 0.8364 (mt) REVERT: K 71 ASP cc_start: 0.8486 (t0) cc_final: 0.8185 (p0) REVERT: H 48 MET cc_start: 0.9207 (mtp) cc_final: 0.8773 (mtt) REVERT: H 63 GLN cc_start: 0.8888 (pm20) cc_final: 0.8009 (pm20) REVERT: B 184 LEU cc_start: 0.8644 (mt) cc_final: 0.8246 (mt) REVERT: E 592 PHE cc_start: 0.8977 (t80) cc_final: 0.8675 (t80) REVERT: L 71 ASP cc_start: 0.8328 (t0) cc_final: 0.7983 (p0) REVERT: L 76 ILE cc_start: 0.9135 (mt) cc_final: 0.8912 (tt) REVERT: I 48 MET cc_start: 0.9243 (mtp) cc_final: 0.8686 (mtp) REVERT: C 99 TYR cc_start: 0.7387 (m-80) cc_final: 0.6879 (m-10) REVERT: C 100 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8572 (tt0) REVERT: C 127 ASP cc_start: 0.8922 (m-30) cc_final: 0.8721 (t0) REVERT: C 184 LEU cc_start: 0.8689 (mt) cc_final: 0.8354 (mt) REVERT: F 592 PHE cc_start: 0.9135 (t80) cc_final: 0.8820 (t80) outliers start: 3 outliers final: 0 residues processed: 336 average time/residue: 0.2676 time to fit residues: 125.2213 Evaluate side-chains 169 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 3.9990 chunk 120 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 13200 Z= 0.383 Angle : 0.834 9.306 17934 Z= 0.435 Chirality : 0.049 0.243 2070 Planarity : 0.006 0.052 2262 Dihedral : 10.475 67.825 2310 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.27 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.22), residues: 1590 helix: -0.19 (0.34), residues: 207 sheet: -0.22 (0.21), residues: 621 loop : 0.55 (0.24), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP I 47 HIS 0.016 0.003 HIS C 154 PHE 0.031 0.003 PHE A 132 TYR 0.029 0.003 TYR B 99 ARG 0.008 0.001 ARG J 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 71 ASP cc_start: 0.8494 (t0) cc_final: 0.7979 (p0) REVERT: G 48 MET cc_start: 0.9325 (mtp) cc_final: 0.8738 (mtp) REVERT: A 111 LEU cc_start: 0.9365 (mt) cc_final: 0.9165 (tt) REVERT: A 162 TYR cc_start: 0.7135 (m-80) cc_final: 0.6680 (m-10) REVERT: D 584 ILE cc_start: 0.9671 (pt) cc_final: 0.9402 (pt) REVERT: D 585 LEU cc_start: 0.9075 (pt) cc_final: 0.8868 (mp) REVERT: K 71 ASP cc_start: 0.8526 (t0) cc_final: 0.8050 (p0) REVERT: H 48 MET cc_start: 0.9271 (mtp) cc_final: 0.8636 (mtp) REVERT: H 63 GLN cc_start: 0.8902 (pm20) cc_final: 0.8628 (pm20) REVERT: B 141 VAL cc_start: 0.9272 (t) cc_final: 0.9069 (p) REVERT: B 162 TYR cc_start: 0.7373 (m-80) cc_final: 0.6908 (m-10) REVERT: E 585 LEU cc_start: 0.8850 (mt) cc_final: 0.8293 (mt) REVERT: E 588 LYS cc_start: 0.9466 (mmtm) cc_final: 0.9232 (mmmt) REVERT: L 4 MET cc_start: 0.8768 (mmt) cc_final: 0.7724 (tpp) REVERT: L 17 GLU cc_start: 0.8977 (pt0) cc_final: 0.8557 (mp0) REVERT: L 71 ASP cc_start: 0.8481 (t0) cc_final: 0.7977 (p0) REVERT: I 48 MET cc_start: 0.9300 (mtp) cc_final: 0.8780 (mtp) REVERT: C 127 ASP cc_start: 0.8950 (m-30) cc_final: 0.8727 (t0) REVERT: C 141 VAL cc_start: 0.9364 (t) cc_final: 0.9149 (p) REVERT: F 592 PHE cc_start: 0.8873 (t80) cc_final: 0.8573 (t80) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.2650 time to fit residues: 87.3716 Evaluate side-chains 148 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 20.0000 chunk 120 optimal weight: 50.0000 chunk 98 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 144 optimal weight: 8.9990 chunk 156 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 116 optimal weight: 0.5980 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 6 GLN ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN ** E 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 1 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 43 GLN ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 13200 Z= 0.280 Angle : 0.705 9.590 17934 Z= 0.370 Chirality : 0.046 0.216 2070 Planarity : 0.005 0.053 2262 Dihedral : 7.643 41.737 2310 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.34 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.22), residues: 1590 helix: 0.03 (0.34), residues: 213 sheet: -0.29 (0.22), residues: 594 loop : 0.10 (0.23), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP I 105 HIS 0.011 0.002 HIS C 154 PHE 0.026 0.002 PHE A 132 TYR 0.034 0.002 TYR B 171 ARG 0.006 0.001 ARG F 580 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 4 MET cc_start: 0.8563 (tpp) cc_final: 0.8106 (mmm) REVERT: J 71 ASP cc_start: 0.8495 (t0) cc_final: 0.8006 (p0) REVERT: G 48 MET cc_start: 0.9319 (mtp) cc_final: 0.8641 (mtp) REVERT: A 162 TYR cc_start: 0.7254 (m-80) cc_final: 0.6724 (m-10) REVERT: A 183 PHE cc_start: 0.8109 (m-80) cc_final: 0.7887 (m-80) REVERT: K 4 MET cc_start: 0.8457 (tpp) cc_final: 0.8098 (mmm) REVERT: K 71 ASP cc_start: 0.8430 (t0) cc_final: 0.8109 (p0) REVERT: H 48 MET cc_start: 0.9193 (mtp) cc_final: 0.8608 (mtp) REVERT: H 63 GLN cc_start: 0.8928 (pm20) cc_final: 0.8611 (pm20) REVERT: B 132 PHE cc_start: 0.6339 (p90) cc_final: 0.5999 (p90) REVERT: B 162 TYR cc_start: 0.7161 (m-80) cc_final: 0.6641 (m-10) REVERT: E 585 LEU cc_start: 0.8882 (mt) cc_final: 0.8354 (mt) REVERT: L 4 MET cc_start: 0.8511 (mmt) cc_final: 0.7701 (tpp) REVERT: L 17 GLU cc_start: 0.9092 (pt0) cc_final: 0.8881 (pt0) REVERT: L 71 ASP cc_start: 0.8538 (t0) cc_final: 0.7954 (p0) REVERT: I 48 MET cc_start: 0.9261 (mtp) cc_final: 0.8617 (mtp) REVERT: C 99 TYR cc_start: 0.7214 (m-80) cc_final: 0.6907 (m-80) REVERT: C 162 TYR cc_start: 0.6926 (m-80) cc_final: 0.6561 (m-80) REVERT: C 270 THR cc_start: 0.8623 (m) cc_final: 0.8350 (p) REVERT: F 577 THR cc_start: 0.8425 (t) cc_final: 0.7775 (t) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.2223 time to fit residues: 68.0088 Evaluate side-chains 143 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 69 optimal weight: 0.0570 chunk 97 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 127 optimal weight: 9.9990 overall best weight: 3.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 1 GLN ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 1 GLN ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN I 43 GLN ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.4831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 13200 Z= 0.368 Angle : 0.712 7.599 17934 Z= 0.371 Chirality : 0.045 0.204 2070 Planarity : 0.006 0.057 2262 Dihedral : 6.451 42.095 2310 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.60 % Favored : 94.34 % Rotamer: Outliers : 0.30 % Allowed : 2.81 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.22), residues: 1590 helix: 0.12 (0.34), residues: 213 sheet: -0.55 (0.21), residues: 594 loop : -0.01 (0.23), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP E 531 HIS 0.010 0.002 HIS C 154 PHE 0.030 0.002 PHE B 132 TYR 0.028 0.003 TYR B 109 ARG 0.011 0.001 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 176 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 4 MET cc_start: 0.8556 (tpp) cc_final: 0.8191 (mmm) REVERT: J 71 ASP cc_start: 0.8482 (t0) cc_final: 0.7956 (p0) REVERT: G 48 MET cc_start: 0.9270 (mtp) cc_final: 0.8271 (mpp) REVERT: A 270 THR cc_start: 0.8322 (m) cc_final: 0.8058 (p) REVERT: K 4 MET cc_start: 0.8479 (tpp) cc_final: 0.8180 (mmm) REVERT: K 71 ASP cc_start: 0.8572 (t0) cc_final: 0.8174 (p0) REVERT: H 48 MET cc_start: 0.9312 (mtp) cc_final: 0.8824 (mtp) REVERT: H 63 GLN cc_start: 0.9001 (pm20) cc_final: 0.8238 (pm20) REVERT: E 585 LEU cc_start: 0.8767 (mt) cc_final: 0.8360 (mt) REVERT: E 588 LYS cc_start: 0.9475 (mmtm) cc_final: 0.9253 (mmmt) REVERT: L 71 ASP cc_start: 0.8469 (t0) cc_final: 0.7780 (p0) REVERT: I 48 MET cc_start: 0.9323 (mtp) cc_final: 0.8761 (mtm) REVERT: C 270 THR cc_start: 0.8544 (m) cc_final: 0.8316 (p) REVERT: F 588 LYS cc_start: 0.9506 (mmtm) cc_final: 0.9294 (mmmt) outliers start: 4 outliers final: 1 residues processed: 180 average time/residue: 0.2241 time to fit residues: 60.0791 Evaluate side-chains 120 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 119 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 2.9990 chunk 2 optimal weight: 20.0000 chunk 114 optimal weight: 5.9990 chunk 63 optimal weight: 30.0000 chunk 131 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 137 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN ** I 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 43 GLN ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.5487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 13200 Z= 0.355 Angle : 0.691 9.385 17934 Z= 0.362 Chirality : 0.045 0.189 2070 Planarity : 0.005 0.046 2262 Dihedral : 6.292 41.096 2310 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.28 % Favored : 94.65 % Rotamer: Outliers : 0.15 % Allowed : 2.22 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.21), residues: 1590 helix: 0.06 (0.33), residues: 213 sheet: -0.61 (0.22), residues: 564 loop : -0.14 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP H 105 HIS 0.008 0.002 HIS C 154 PHE 0.030 0.002 PHE B 132 TYR 0.028 0.002 TYR C 99 ARG 0.008 0.001 ARG B 85 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 168 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 4 MET cc_start: 0.8246 (tpp) cc_final: 0.7937 (mmm) REVERT: J 71 ASP cc_start: 0.8486 (t0) cc_final: 0.7907 (p0) REVERT: G 48 MET cc_start: 0.9336 (mtp) cc_final: 0.8392 (mpp) REVERT: A 100 GLU cc_start: 0.8604 (tt0) cc_final: 0.8225 (tt0) REVERT: A 109 TYR cc_start: 0.8978 (m-80) cc_final: 0.8645 (m-80) REVERT: A 161 LEU cc_start: 0.9090 (mt) cc_final: 0.8795 (mt) REVERT: A 270 THR cc_start: 0.8402 (m) cc_final: 0.8169 (p) REVERT: D 531 TRP cc_start: 0.8545 (p-90) cc_final: 0.8339 (p-90) REVERT: D 592 PHE cc_start: 0.9345 (t80) cc_final: 0.9069 (t80) REVERT: K 4 MET cc_start: 0.8538 (tpp) cc_final: 0.8222 (mmm) REVERT: K 71 ASP cc_start: 0.8468 (t0) cc_final: 0.7964 (p0) REVERT: H 48 MET cc_start: 0.9344 (mtp) cc_final: 0.8905 (mtp) REVERT: H 63 GLN cc_start: 0.9100 (pm20) cc_final: 0.8427 (pm20) REVERT: B 132 PHE cc_start: 0.6705 (p90) cc_final: 0.6471 (p90) REVERT: E 588 LYS cc_start: 0.9485 (mmtm) cc_final: 0.9260 (mmmt) REVERT: L 17 GLU cc_start: 0.9140 (pt0) cc_final: 0.8911 (mp0) REVERT: L 71 ASP cc_start: 0.8486 (t0) cc_final: 0.7759 (p0) REVERT: I 48 MET cc_start: 0.9374 (mtp) cc_final: 0.8854 (mtm) outliers start: 2 outliers final: 1 residues processed: 169 average time/residue: 0.2453 time to fit residues: 63.3007 Evaluate side-chains 113 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 112 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 chunk 153 optimal weight: 0.0470 chunk 127 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 148 optimal weight: 7.9990 overall best weight: 2.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 91 GLN ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 43 GLN ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.5727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13200 Z= 0.246 Angle : 0.630 10.736 17934 Z= 0.327 Chirality : 0.044 0.166 2070 Planarity : 0.005 0.040 2262 Dihedral : 6.055 38.892 2310 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.35 % Favored : 94.59 % Rotamer: Outliers : 0.07 % Allowed : 2.00 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.22), residues: 1590 helix: 0.45 (0.36), residues: 213 sheet: -0.61 (0.22), residues: 591 loop : -0.07 (0.23), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 104 HIS 0.006 0.001 HIS C 154 PHE 0.026 0.002 PHE B 132 TYR 0.023 0.002 TYR C 99 ARG 0.008 0.001 ARG B 85 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 164 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 4 MET cc_start: 0.8351 (tpp) cc_final: 0.7957 (mmm) REVERT: J 48 LEU cc_start: 0.8615 (mt) cc_final: 0.8415 (mt) REVERT: J 71 ASP cc_start: 0.8485 (t0) cc_final: 0.7894 (p0) REVERT: G 48 MET cc_start: 0.9348 (mtp) cc_final: 0.8379 (mpp) REVERT: A 99 TYR cc_start: 0.6605 (m-80) cc_final: 0.6250 (m-80) REVERT: A 109 TYR cc_start: 0.9039 (m-80) cc_final: 0.8757 (m-80) REVERT: A 270 THR cc_start: 0.8344 (m) cc_final: 0.8110 (p) REVERT: D 592 PHE cc_start: 0.9357 (t80) cc_final: 0.9069 (t80) REVERT: K 4 MET cc_start: 0.8536 (tpp) cc_final: 0.8215 (mmm) REVERT: K 71 ASP cc_start: 0.8412 (t0) cc_final: 0.7879 (p0) REVERT: H 48 MET cc_start: 0.9356 (mtp) cc_final: 0.8913 (mtp) REVERT: H 63 GLN cc_start: 0.9120 (pm20) cc_final: 0.8486 (pm20) REVERT: B 132 PHE cc_start: 0.6666 (p90) cc_final: 0.6464 (p90) REVERT: E 585 LEU cc_start: 0.8893 (mt) cc_final: 0.8583 (mt) REVERT: L 17 GLU cc_start: 0.9278 (pt0) cc_final: 0.8885 (mp0) REVERT: L 71 ASP cc_start: 0.8489 (t0) cc_final: 0.7722 (p0) REVERT: I 48 MET cc_start: 0.9357 (mtp) cc_final: 0.8468 (mpp) REVERT: C 99 TYR cc_start: 0.7029 (m-80) cc_final: 0.6631 (m-80) REVERT: C 161 LEU cc_start: 0.8820 (mp) cc_final: 0.8577 (mp) REVERT: F 588 LYS cc_start: 0.9539 (mmtm) cc_final: 0.9330 (mmmt) outliers start: 1 outliers final: 1 residues processed: 165 average time/residue: 0.2235 time to fit residues: 55.6098 Evaluate side-chains 111 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 112 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 153 optimal weight: 0.0000 chunk 95 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 61 optimal weight: 9.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 27 GLN ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 ASN ** E 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 43 GLN C 139 HIS ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.5991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13200 Z= 0.214 Angle : 0.631 11.082 17934 Z= 0.322 Chirality : 0.044 0.200 2070 Planarity : 0.005 0.039 2262 Dihedral : 5.902 37.102 2310 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.97 % Favored : 94.97 % Rotamer: Outliers : 0.07 % Allowed : 1.19 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.22), residues: 1590 helix: 0.24 (0.35), residues: 213 sheet: -0.62 (0.22), residues: 606 loop : -0.08 (0.24), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 531 HIS 0.005 0.001 HIS C 139 PHE 0.026 0.002 PHE E 535 TYR 0.031 0.002 TYR C 109 ARG 0.009 0.001 ARG H 84 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 153 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 4 MET cc_start: 0.8354 (tpp) cc_final: 0.7953 (mmm) REVERT: J 71 ASP cc_start: 0.8506 (t0) cc_final: 0.7907 (p0) REVERT: G 48 MET cc_start: 0.9353 (mtp) cc_final: 0.8376 (mpp) REVERT: G 66 ASP cc_start: 0.8747 (m-30) cc_final: 0.8511 (m-30) REVERT: A 99 TYR cc_start: 0.7235 (m-80) cc_final: 0.7002 (m-80) REVERT: D 592 PHE cc_start: 0.9347 (t80) cc_final: 0.9084 (t80) REVERT: K 4 MET cc_start: 0.8554 (tpp) cc_final: 0.8203 (mmm) REVERT: K 71 ASP cc_start: 0.8458 (t0) cc_final: 0.7963 (p0) REVERT: H 48 MET cc_start: 0.9352 (mtp) cc_final: 0.8906 (mtp) REVERT: H 63 GLN cc_start: 0.9092 (pm20) cc_final: 0.8505 (pm20) REVERT: H 93 MET cc_start: 0.8795 (tpp) cc_final: 0.8406 (tpp) REVERT: B 132 PHE cc_start: 0.6565 (p90) cc_final: 0.6326 (p90) REVERT: E 585 LEU cc_start: 0.8885 (mt) cc_final: 0.8600 (mt) REVERT: L 17 GLU cc_start: 0.9311 (pt0) cc_final: 0.8970 (mp0) REVERT: L 71 ASP cc_start: 0.8492 (t0) cc_final: 0.7727 (p0) REVERT: I 48 MET cc_start: 0.9348 (mtp) cc_final: 0.8462 (mpp) REVERT: C 162 TYR cc_start: 0.7152 (m-80) cc_final: 0.6839 (m-80) REVERT: F 588 LYS cc_start: 0.9474 (mmtm) cc_final: 0.9259 (mmmt) outliers start: 1 outliers final: 0 residues processed: 154 average time/residue: 0.2442 time to fit residues: 56.4850 Evaluate side-chains 111 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 29 optimal weight: 7.9990 chunk 97 optimal weight: 0.0870 chunk 104 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 120 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 overall best weight: 1.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 43 GLN ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.6201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13200 Z= 0.200 Angle : 0.608 9.399 17934 Z= 0.311 Chirality : 0.044 0.181 2070 Planarity : 0.004 0.039 2262 Dihedral : 5.630 35.036 2310 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.03 % Favored : 94.91 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.22), residues: 1590 helix: 0.20 (0.36), residues: 213 sheet: -0.42 (0.22), residues: 576 loop : -0.18 (0.23), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 104 HIS 0.004 0.001 HIS E 516 PHE 0.023 0.001 PHE B 132 TYR 0.017 0.002 TYR C 99 ARG 0.011 0.001 ARG D 574 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 4 MET cc_start: 0.8369 (tpp) cc_final: 0.7955 (mmm) REVERT: J 71 ASP cc_start: 0.8514 (t0) cc_final: 0.7894 (p0) REVERT: G 48 MET cc_start: 0.9348 (mtp) cc_final: 0.8390 (mpp) REVERT: G 93 MET cc_start: 0.8743 (tpp) cc_final: 0.8308 (tpp) REVERT: A 99 TYR cc_start: 0.7108 (m-80) cc_final: 0.6788 (m-80) REVERT: A 109 TYR cc_start: 0.8977 (m-80) cc_final: 0.8629 (m-80) REVERT: A 162 TYR cc_start: 0.6957 (m-80) cc_final: 0.6723 (m-80) REVERT: A 180 VAL cc_start: 0.7638 (m) cc_final: 0.7283 (m) REVERT: D 592 PHE cc_start: 0.9356 (t80) cc_final: 0.9090 (t80) REVERT: K 71 ASP cc_start: 0.8509 (t0) cc_final: 0.7908 (p0) REVERT: H 48 MET cc_start: 0.9346 (mtp) cc_final: 0.8916 (mtp) REVERT: H 63 GLN cc_start: 0.9128 (pm20) cc_final: 0.8604 (pm20) REVERT: B 132 PHE cc_start: 0.6450 (p90) cc_final: 0.6239 (p90) REVERT: L 17 GLU cc_start: 0.9262 (pt0) cc_final: 0.8956 (mp0) REVERT: I 48 MET cc_start: 0.9334 (mtp) cc_final: 0.8459 (mpp) REVERT: I 93 MET cc_start: 0.9002 (tpt) cc_final: 0.8693 (tpp) REVERT: C 99 TYR cc_start: 0.7170 (m-80) cc_final: 0.6814 (m-80) REVERT: C 162 TYR cc_start: 0.6913 (m-80) cc_final: 0.6529 (m-80) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.2410 time to fit residues: 54.6863 Evaluate side-chains 114 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 10.0000 chunk 142 optimal weight: 5.9990 chunk 146 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 112 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 129 optimal weight: 9.9990 chunk 135 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 43 GLN ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.6467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13200 Z= 0.245 Angle : 0.614 7.959 17934 Z= 0.316 Chirality : 0.043 0.171 2070 Planarity : 0.004 0.038 2262 Dihedral : 5.650 35.176 2310 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.47 % Favored : 94.40 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.22), residues: 1590 helix: 0.27 (0.36), residues: 213 sheet: -0.46 (0.22), residues: 576 loop : -0.20 (0.23), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 104 HIS 0.005 0.001 HIS B 154 PHE 0.024 0.002 PHE B 132 TYR 0.019 0.002 TYR C 99 ARG 0.007 0.001 ARG D 574 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 4 MET cc_start: 0.8398 (tpp) cc_final: 0.7972 (mmm) REVERT: G 48 MET cc_start: 0.9367 (mtp) cc_final: 0.8452 (mpp) REVERT: A 99 TYR cc_start: 0.7339 (m-80) cc_final: 0.7015 (m-80) REVERT: A 109 TYR cc_start: 0.9031 (m-80) cc_final: 0.8643 (m-10) REVERT: H 48 MET cc_start: 0.9352 (mtp) cc_final: 0.8951 (mtp) REVERT: H 63 GLN cc_start: 0.9128 (pm20) cc_final: 0.8596 (pm20) REVERT: H 93 MET cc_start: 0.8534 (tpp) cc_final: 0.8164 (tpp) REVERT: L 4 MET cc_start: 0.8394 (tpt) cc_final: 0.6992 (tpt) REVERT: I 48 MET cc_start: 0.9396 (mtp) cc_final: 0.9019 (mtp) REVERT: C 99 TYR cc_start: 0.7215 (m-80) cc_final: 0.6880 (m-80) REVERT: C 109 TYR cc_start: 0.8952 (m-80) cc_final: 0.8648 (m-80) REVERT: C 162 TYR cc_start: 0.7124 (m-80) cc_final: 0.6754 (m-80) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.2204 time to fit residues: 47.3092 Evaluate side-chains 112 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 158 optimal weight: 0.9990 chunk 145 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 97 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 chunk 100 optimal weight: 7.9990 chunk 134 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 43 GLN ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.6618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13200 Z= 0.213 Angle : 0.604 7.449 17934 Z= 0.309 Chirality : 0.043 0.170 2070 Planarity : 0.004 0.038 2262 Dihedral : 5.542 33.928 2310 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.78 % Favored : 95.03 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.22), residues: 1590 helix: 0.13 (0.36), residues: 219 sheet: -0.46 (0.22), residues: 576 loop : -0.20 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 104 HIS 0.005 0.001 HIS E 516 PHE 0.022 0.002 PHE B 132 TYR 0.017 0.002 TYR D 517 ARG 0.008 0.001 ARG D 574 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 48 MET cc_start: 0.9371 (mtp) cc_final: 0.8461 (mpp) REVERT: G 93 MET cc_start: 0.8518 (tpp) cc_final: 0.8112 (tpp) REVERT: A 109 TYR cc_start: 0.9014 (m-80) cc_final: 0.8654 (m-10) REVERT: H 48 MET cc_start: 0.9338 (mtp) cc_final: 0.8940 (mtp) REVERT: H 63 GLN cc_start: 0.9203 (pm20) cc_final: 0.8737 (pm20) REVERT: H 93 MET cc_start: 0.8589 (tpp) cc_final: 0.8224 (tpp) REVERT: B 132 PHE cc_start: 0.6432 (p90) cc_final: 0.6133 (p90) REVERT: B 219 ARG cc_start: 0.9313 (ttp-110) cc_final: 0.8982 (ttp80) REVERT: L 4 MET cc_start: 0.8239 (tpt) cc_final: 0.6984 (tpt) REVERT: I 48 MET cc_start: 0.9390 (mtp) cc_final: 0.9010 (mtp) REVERT: I 93 MET cc_start: 0.8691 (tpp) cc_final: 0.8059 (tpp) REVERT: C 99 TYR cc_start: 0.7135 (m-80) cc_final: 0.6925 (m-80) REVERT: C 162 TYR cc_start: 0.6952 (m-80) cc_final: 0.6556 (m-80) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.2159 time to fit residues: 46.4084 Evaluate side-chains 112 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 7.9990 chunk 116 optimal weight: 20.0000 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 126 optimal weight: 0.7980 chunk 52 optimal weight: 9.9990 chunk 129 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 560 GLN ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 586 ASN I 43 GLN ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.051175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.042154 restraints weight = 109324.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.043431 restraints weight = 70951.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.044367 restraints weight = 52382.376| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.6959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 13200 Z= 0.331 Angle : 0.683 9.238 17934 Z= 0.353 Chirality : 0.044 0.155 2070 Planarity : 0.005 0.042 2262 Dihedral : 5.920 38.592 2310 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.16 % Favored : 93.65 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.21), residues: 1590 helix: -0.05 (0.35), residues: 219 sheet: -0.62 (0.21), residues: 621 loop : -0.41 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 104 HIS 0.009 0.002 HIS E 516 PHE 0.020 0.002 PHE B 132 TYR 0.023 0.002 TYR B 99 ARG 0.008 0.001 ARG H 84 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2444.65 seconds wall clock time: 45 minutes 17.76 seconds (2717.76 seconds total)