Starting phenix.real_space_refine on Thu Feb 15 15:21:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s1x_24807/02_2024/7s1x_24807_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s1x_24807/02_2024/7s1x_24807.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s1x_24807/02_2024/7s1x_24807.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s1x_24807/02_2024/7s1x_24807.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s1x_24807/02_2024/7s1x_24807_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s1x_24807/02_2024/7s1x_24807_updated.pdb" } resolution = 2.9 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= 0.009 sd= 0.148 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 2 8.98 5 S 74 5.16 5 Cl 2 4.86 5 C 8264 2.51 5 N 2130 2.21 5 O 2186 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 219": "OD1" <-> "OD2" Residue "B TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 307": "NH1" <-> "NH2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 389": "OE1" <-> "OE2" Residue "B PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 810": "OD1" <-> "OD2" Residue "B PHE 811": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 854": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 901": "OD1" <-> "OD2" Residue "B PHE 907": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1069": "NH1" <-> "NH2" Residue "B PHE 1210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 219": "OD1" <-> "OD2" Residue "A TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 389": "OE1" <-> "OE2" Residue "A PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 810": "OD1" <-> "OD2" Residue "A PHE 811": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 854": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 901": "OD1" <-> "OD2" Residue "A PHE 907": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1069": "NH1" <-> "NH2" Residue "A PHE 1210": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12658 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 6302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 871, 6302 Classifications: {'peptide': 871} Incomplete info: {'backbone_only': 29, 'truncation_to_alanine': 117} Link IDs: {'PTRANS': 31, 'TRANS': 839} Chain breaks: 2 Unresolved non-hydrogen bonds: 525 Unresolved non-hydrogen angles: 666 Unresolved non-hydrogen dihedrals: 393 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 14, 'ASP:plan': 19, 'PHE:plan': 2, 'GLU:plan': 26, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 283 Chain: "A" Number of atoms: 6302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 871, 6302 Classifications: {'peptide': 871} Incomplete info: {'backbone_only': 29, 'truncation_to_alanine': 117} Link IDs: {'PTRANS': 31, 'TRANS': 839} Chain breaks: 2 Unresolved non-hydrogen bonds: 525 Unresolved non-hydrogen angles: 666 Unresolved non-hydrogen dihedrals: 393 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 14, 'ASP:plan': 19, 'PHE:plan': 2, 'GLU:plan': 26, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 283 Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 27 Unusual residues: {' K': 1, ' CL': 1, '82U': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 27 Unusual residues: {' K': 1, ' CL': 1, '82U': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.09, per 1000 atoms: 0.56 Number of scatterers: 12658 At special positions: 0 Unit cell: (111.3, 107.06, 145.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 2 19.00 Cl 2 17.00 S 74 16.00 O 2186 8.00 N 2130 7.00 C 8264 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 563 " - pdb=" SG CYS B 568 " distance=2.03 Simple disulfide: pdb=" SG CYS B 577 " - pdb=" SG CYS B 582 " distance=2.03 Simple disulfide: pdb=" SG CYS A 563 " - pdb=" SG CYS A 568 " distance=2.03 Simple disulfide: pdb=" SG CYS A 577 " - pdb=" SG CYS A 582 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.44 Conformation dependent library (CDL) restraints added in 2.2 seconds 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB 82U B1301 " pdb=" CB 82U A1301 " Number of C-beta restraints generated: 3124 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 73 helices and 4 sheets defined 57.1% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.93 Creating SS restraints... Processing helix chain 'B' and resid 224 through 227 Processing helix chain 'B' and resid 243 through 247 Processing helix chain 'B' and resid 287 through 290 No H-bonds generated for 'chain 'B' and resid 287 through 290' Processing helix chain 'B' and resid 292 through 299 Processing helix chain 'B' and resid 302 through 305 No H-bonds generated for 'chain 'B' and resid 302 through 305' Processing helix chain 'B' and resid 308 through 314 Processing helix chain 'B' and resid 317 through 342 removed outlier: 3.923A pdb=" N LEU B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 397 Proline residue: B 362 - end of helix removed outlier: 3.862A pdb=" N ALA B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 424 removed outlier: 4.517A pdb=" N ARG B 410 " --> pdb=" O ILE B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 453 Processing helix chain 'B' and resid 470 through 476 Processing helix chain 'B' and resid 487 through 498 Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 505 through 510 removed outlier: 4.831A pdb=" N GLY B 509 " --> pdb=" O ASN B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 543 removed outlier: 4.218A pdb=" N LEU B 524 " --> pdb=" O LYS B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 570 No H-bonds generated for 'chain 'B' and resid 567 through 570' Processing helix chain 'B' and resid 591 through 596 removed outlier: 4.122A pdb=" N VAL B 596 " --> pdb=" O MET B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 631 removed outlier: 3.942A pdb=" N GLY B 606 " --> pdb=" O LEU B 602 " (cutoff:3.500A) Proline residue: B 623 - end of helix Processing helix chain 'B' and resid 636 through 638 No H-bonds generated for 'chain 'B' and resid 636 through 638' Processing helix chain 'B' and resid 652 through 668 Processing helix chain 'B' and resid 671 through 698 Proline residue: B 676 - end of helix Processing helix chain 'B' and resid 713 through 729 Processing helix chain 'B' and resid 732 through 752 Processing helix chain 'B' and resid 761 through 779 removed outlier: 3.523A pdb=" N GLY B 779 " --> pdb=" O ILE B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 786 No H-bonds generated for 'chain 'B' and resid 784 through 786' Processing helix chain 'B' and resid 802 through 810 Processing helix chain 'B' and resid 828 through 848 removed outlier: 3.727A pdb=" N LYS B 833 " --> pdb=" O ARG B 829 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA B 840 " --> pdb=" O SER B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 873 Processing helix chain 'B' and resid 877 through 879 No H-bonds generated for 'chain 'B' and resid 877 through 879' Processing helix chain 'B' and resid 897 through 912 Processing helix chain 'B' and resid 1035 through 1045 Proline residue: B1040 - end of helix Processing helix chain 'B' and resid 1047 through 1049 No H-bonds generated for 'chain 'B' and resid 1047 through 1049' Processing helix chain 'B' and resid 1065 through 1078 Processing helix chain 'B' and resid 1098 through 1111 Proline residue: B1110 - end of helix Processing helix chain 'B' and resid 1121 through 1128 Processing helix chain 'B' and resid 1135 through 1139 removed outlier: 3.590A pdb=" N LEU B1139 " --> pdb=" O THR B1135 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1135 through 1139' Processing helix chain 'B' and resid 1142 through 1162 removed outlier: 3.979A pdb=" N SER B1161 " --> pdb=" O LYS B1157 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR B1162 " --> pdb=" O GLU B1158 " (cutoff:3.500A) Processing helix chain 'B' and resid 1180 through 1191 Processing helix chain 'A' and resid 224 through 227 Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 287 through 290 No H-bonds generated for 'chain 'A' and resid 287 through 290' Processing helix chain 'A' and resid 292 through 299 Processing helix chain 'A' and resid 302 through 305 No H-bonds generated for 'chain 'A' and resid 302 through 305' Processing helix chain 'A' and resid 308 through 314 Processing helix chain 'A' and resid 317 through 342 removed outlier: 3.923A pdb=" N LEU A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 397 Proline residue: A 362 - end of helix removed outlier: 3.862A pdb=" N ALA A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 424 removed outlier: 4.518A pdb=" N ARG A 410 " --> pdb=" O ILE A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 453 Processing helix chain 'A' and resid 470 through 476 Processing helix chain 'A' and resid 487 through 498 Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 505 through 510 removed outlier: 4.831A pdb=" N GLY A 509 " --> pdb=" O ASN A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 543 removed outlier: 4.217A pdb=" N LEU A 524 " --> pdb=" O LYS A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 570 No H-bonds generated for 'chain 'A' and resid 567 through 570' Processing helix chain 'A' and resid 591 through 596 removed outlier: 4.122A pdb=" N VAL A 596 " --> pdb=" O MET A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 631 removed outlier: 3.943A pdb=" N GLY A 606 " --> pdb=" O LEU A 602 " (cutoff:3.500A) Proline residue: A 623 - end of helix Processing helix chain 'A' and resid 636 through 638 No H-bonds generated for 'chain 'A' and resid 636 through 638' Processing helix chain 'A' and resid 652 through 668 Processing helix chain 'A' and resid 671 through 698 Proline residue: A 676 - end of helix Processing helix chain 'A' and resid 713 through 729 Processing helix chain 'A' and resid 732 through 752 Processing helix chain 'A' and resid 761 through 779 removed outlier: 3.523A pdb=" N GLY A 779 " --> pdb=" O ILE A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 786 No H-bonds generated for 'chain 'A' and resid 784 through 786' Processing helix chain 'A' and resid 802 through 810 Processing helix chain 'A' and resid 828 through 848 removed outlier: 3.727A pdb=" N LYS A 833 " --> pdb=" O ARG A 829 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A 840 " --> pdb=" O SER A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 873 Processing helix chain 'A' and resid 877 through 879 No H-bonds generated for 'chain 'A' and resid 877 through 879' Processing helix chain 'A' and resid 897 through 912 Processing helix chain 'A' and resid 1035 through 1045 Proline residue: A1040 - end of helix Processing helix chain 'A' and resid 1065 through 1078 Processing helix chain 'A' and resid 1098 through 1111 Proline residue: A1110 - end of helix Processing helix chain 'A' and resid 1121 through 1128 Processing helix chain 'A' and resid 1135 through 1139 removed outlier: 3.591A pdb=" N LEU A1139 " --> pdb=" O THR A1135 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1135 through 1139' Processing helix chain 'A' and resid 1142 through 1162 removed outlier: 3.978A pdb=" N SER A1161 " --> pdb=" O LYS A1157 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N THR A1162 " --> pdb=" O GLU A1158 " (cutoff:3.500A) Processing helix chain 'A' and resid 1180 through 1191 Processing sheet with id= A, first strand: chain 'B' and resid 1024 through 1027 removed outlier: 6.133A pdb=" N ILE B1165 " --> pdb=" O ASP B1025 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N TRP B1027 " --> pdb=" O ILE B1165 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL B1167 " --> pdb=" O TRP B1027 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE B 854 " --> pdb=" O CYS B 820 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N HIS B 822 " --> pdb=" O PHE B 854 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ALA B 856 " --> pdb=" O HIS B 822 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N HIS B 824 " --> pdb=" O ALA B 856 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL B 858 " --> pdb=" O HIS B 824 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 1056 through 1059 Processing sheet with id= C, first strand: chain 'A' and resid 1024 through 1027 removed outlier: 6.133A pdb=" N ILE A1165 " --> pdb=" O ASP A1025 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N TRP A1027 " --> pdb=" O ILE A1165 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL A1167 " --> pdb=" O TRP A1027 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE A 854 " --> pdb=" O CYS A 820 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N HIS A 822 " --> pdb=" O PHE A 854 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ALA A 856 " --> pdb=" O HIS A 822 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N HIS A 824 " --> pdb=" O ALA A 856 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL A 858 " --> pdb=" O HIS A 824 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1056 through 1059 698 hydrogen bonds defined for protein. 2058 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: 4.09 Time building geometry restraints manager: 5.70 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: 3964 1.34 - 1.46: 2241 1.46 - 1.58: 6627 1.58 - 1.69: 0 1.69 - 1.81: 122 Bond restraints: 12954 Sorted by residual: bond pdb=" N 82U A1301 " pdb=" CA 82U A1301 " ideal model delta sigma weight residual 1.366 1.443 -0.077 2.00e-02 2.50e+03 1.50e+01 bond pdb=" N 82U B1301 " pdb=" CA 82U B1301 " ideal model delta sigma weight residual 1.366 1.443 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" NE1 82U B1301 " pdb=" S1 82U B1301 " ideal model delta sigma weight residual 1.647 1.705 -0.058 2.00e-02 2.50e+03 8.31e+00 bond pdb=" NE1 82U A1301 " pdb=" S1 82U A1301 " ideal model delta sigma weight residual 1.647 1.704 -0.057 2.00e-02 2.50e+03 8.07e+00 bond pdb=" C17 82U A1301 " pdb=" O4 82U A1301 " ideal model delta sigma weight residual 1.245 1.294 -0.049 2.00e-02 2.50e+03 5.97e+00 ... (remaining 12949 not shown) Histogram of bond angle deviations from ideal: 98.57 - 105.68: 265 105.68 - 112.78: 6968 112.78 - 119.89: 4215 119.89 - 126.99: 6048 126.99 - 134.10: 168 Bond angle restraints: 17664 Sorted by residual: angle pdb=" C HIS B 229 " pdb=" N THR B 230 " pdb=" CA THR B 230 " ideal model delta sigma weight residual 121.54 128.88 -7.34 1.91e+00 2.74e-01 1.48e+01 angle pdb=" C HIS A 229 " pdb=" N THR A 230 " pdb=" CA THR A 230 " ideal model delta sigma weight residual 121.54 128.88 -7.34 1.91e+00 2.74e-01 1.48e+01 angle pdb=" C TRP B1027 " pdb=" N TRP B1028 " pdb=" CA TRP B1028 " ideal model delta sigma weight residual 123.12 117.81 5.31 1.52e+00 4.33e-01 1.22e+01 angle pdb=" C TRP A1027 " pdb=" N TRP A1028 " pdb=" CA TRP A1028 " ideal model delta sigma weight residual 123.12 117.82 5.30 1.52e+00 4.33e-01 1.21e+01 angle pdb=" C VAL A1026 " pdb=" N TRP A1027 " pdb=" CA TRP A1027 " ideal model delta sigma weight residual 123.23 117.77 5.46 1.57e+00 4.06e-01 1.21e+01 ... (remaining 17659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.25: 6797 15.25 - 30.50: 496 30.50 - 45.75: 109 45.75 - 61.00: 18 61.00 - 76.25: 16 Dihedral angle restraints: 7436 sinusoidal: 2520 harmonic: 4916 Sorted by residual: dihedral pdb=" CB CYS B 577 " pdb=" SG CYS B 577 " pdb=" SG CYS B 582 " pdb=" CB CYS B 582 " ideal model delta sinusoidal sigma weight residual 93.00 21.73 71.27 1 1.00e+01 1.00e-02 6.52e+01 dihedral pdb=" CB CYS A 577 " pdb=" SG CYS A 577 " pdb=" SG CYS A 582 " pdb=" CB CYS A 582 " ideal model delta sinusoidal sigma weight residual 93.00 21.75 71.25 1 1.00e+01 1.00e-02 6.51e+01 dihedral pdb=" CA THR A 795 " pdb=" C THR A 795 " pdb=" N GLY A 796 " pdb=" CA GLY A 796 " ideal model delta harmonic sigma weight residual -180.00 -155.17 -24.83 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 7433 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1506 0.052 - 0.105: 462 0.105 - 0.157: 81 0.157 - 0.210: 11 0.210 - 0.262: 2 Chirality restraints: 2062 Sorted by residual: chirality pdb=" CG LEU B1156 " pdb=" CB LEU B1156 " pdb=" CD1 LEU B1156 " pdb=" CD2 LEU B1156 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CG LEU A1156 " pdb=" CB LEU A1156 " pdb=" CD1 LEU A1156 " pdb=" CD2 LEU A1156 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA ARG B 705 " pdb=" N ARG B 705 " pdb=" C ARG B 705 " pdb=" CB ARG B 705 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.40e-01 ... (remaining 2059 not shown) Planarity restraints: 2216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A1027 " 0.039 2.00e-02 2.50e+03 4.25e-02 4.52e+01 pdb=" CG TRP A1027 " -0.109 2.00e-02 2.50e+03 pdb=" CD1 TRP A1027 " 0.066 2.00e-02 2.50e+03 pdb=" CD2 TRP A1027 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A1027 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP A1027 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A1027 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1027 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1027 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP A1027 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B1027 " -0.038 2.00e-02 2.50e+03 4.24e-02 4.50e+01 pdb=" CG TRP B1027 " 0.109 2.00e-02 2.50e+03 pdb=" CD1 TRP B1027 " -0.066 2.00e-02 2.50e+03 pdb=" CD2 TRP B1027 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP B1027 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP B1027 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B1027 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1027 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1027 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP B1027 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1028 " -0.035 2.00e-02 2.50e+03 3.34e-02 2.78e+01 pdb=" CG TRP A1028 " 0.084 2.00e-02 2.50e+03 pdb=" CD1 TRP A1028 " -0.047 2.00e-02 2.50e+03 pdb=" CD2 TRP A1028 " 0.011 2.00e-02 2.50e+03 pdb=" NE1 TRP A1028 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A1028 " 0.014 2.00e-02 2.50e+03 pdb=" CE3 TRP A1028 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1028 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1028 " -0.016 2.00e-02 2.50e+03 pdb=" CH2 TRP A1028 " -0.005 2.00e-02 2.50e+03 ... (remaining 2213 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.67: 224 2.67 - 3.29: 15571 3.29 - 3.90: 25612 3.90 - 4.52: 34738 4.52 - 5.14: 52465 Nonbonded interactions: 128610 Sorted by model distance: nonbonded pdb=" NH1 ARG B 705 " pdb=" O PHE A1079 " model vdw 2.052 2.520 nonbonded pdb=" O PHE B1079 " pdb=" NH1 ARG A 705 " model vdw 2.053 2.520 nonbonded pdb=" OH TYR B 686 " pdb="CL CL B1303 " model vdw 2.061 2.590 nonbonded pdb=" OH TYR A 686 " pdb="CL CL A1303 " model vdw 2.061 2.590 nonbonded pdb=" OD2 ASP B1032 " pdb=" OG1 THR B1036 " model vdw 2.138 2.440 ... (remaining 128605 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.780 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: 4.230 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 36.630 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.070 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:12.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 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 : 0.005 0.077 12954 Z= 0.362 Angle : 0.832 10.784 17664 Z= 0.442 Chirality : 0.051 0.262 2062 Planarity : 0.005 0.063 2216 Dihedral : 12.055 76.247 4300 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.88 % Favored : 90.12 % Rotamer: Outliers : 0.17 % Allowed : 0.51 % Favored : 99.32 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.20), residues: 1730 helix: 0.74 (0.16), residues: 982 sheet: -0.13 (0.57), residues: 92 loop : -2.36 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.109 0.007 TRP A1027 HIS 0.010 0.003 HIS B1067 PHE 0.055 0.003 PHE A 608 TYR 0.018 0.002 TYR A 353 ARG 0.009 0.001 ARG A 546 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 338 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 242 SER cc_start: 0.7446 (t) cc_final: 0.7070 (m) REVERT: B 346 PHE cc_start: 0.7749 (t80) cc_final: 0.7449 (t80) REVERT: B 485 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8112 (mm-30) REVERT: B 492 GLU cc_start: 0.7120 (tm-30) cc_final: 0.5853 (mt-10) REVERT: B 543 CYS cc_start: 0.7573 (t) cc_final: 0.6898 (m) REVERT: B 762 THR cc_start: 0.8076 (m) cc_final: 0.7692 (p) REVERT: B 1205 GLN cc_start: 0.7637 (mm-40) cc_final: 0.7349 (mm-40) REVERT: A 242 SER cc_start: 0.7330 (t) cc_final: 0.6944 (m) REVERT: A 346 PHE cc_start: 0.7726 (t80) cc_final: 0.7434 (t80) REVERT: A 485 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8067 (mm-30) REVERT: A 492 GLU cc_start: 0.7047 (tm-30) cc_final: 0.5750 (mt-10) REVERT: A 531 LEU cc_start: 0.6300 (tp) cc_final: 0.6020 (mp) REVERT: A 543 CYS cc_start: 0.7553 (t) cc_final: 0.6954 (m) REVERT: A 762 THR cc_start: 0.8077 (m) cc_final: 0.7689 (p) REVERT: A 879 MET cc_start: 0.8292 (mtt) cc_final: 0.8082 (mtm) REVERT: A 1205 GLN cc_start: 0.7646 (mm-40) cc_final: 0.7367 (mm-40) outliers start: 2 outliers final: 0 residues processed: 340 average time/residue: 0.9210 time to fit residues: 350.0965 Evaluate side-chains 219 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 88 optimal weight: 10.0000 chunk 70 optimal weight: 0.0980 chunk 136 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 GLN ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 589 ASN B 731 ASN B 799 ASN B 806 HIS B1149 GLN B1159 HIS A 435 GLN ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 ASN A 731 ASN A 799 ASN A 806 HIS A1149 GLN A1159 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12954 Z= 0.216 Angle : 0.639 10.697 17664 Z= 0.329 Chirality : 0.044 0.169 2062 Planarity : 0.004 0.050 2216 Dihedral : 5.137 21.300 1880 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 3.63 % Allowed : 12.92 % Favored : 83.45 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.20), residues: 1730 helix: 1.04 (0.17), residues: 976 sheet: 0.01 (0.57), residues: 92 loop : -2.29 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A1027 HIS 0.005 0.001 HIS B 859 PHE 0.036 0.002 PHE A 608 TYR 0.016 0.002 TYR A 353 ARG 0.008 0.001 ARG A1069 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 251 time to evaluate : 1.229 Fit side-chains REVERT: B 242 SER cc_start: 0.7435 (t) cc_final: 0.7089 (m) REVERT: B 346 PHE cc_start: 0.7788 (t80) cc_final: 0.7565 (t80) REVERT: B 430 TRP cc_start: 0.6980 (m100) cc_final: 0.6770 (t-100) REVERT: B 485 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8151 (mm-30) REVERT: B 492 GLU cc_start: 0.7044 (tm-30) cc_final: 0.5690 (mt-10) REVERT: B 543 CYS cc_start: 0.7330 (t) cc_final: 0.6688 (m) REVERT: B 762 THR cc_start: 0.7967 (m) cc_final: 0.7693 (p) REVERT: B 834 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6864 (mp0) REVERT: B 868 GLN cc_start: 0.8368 (tp-100) cc_final: 0.8108 (tp40) REVERT: B 889 LYS cc_start: 0.8225 (tttp) cc_final: 0.7964 (tttp) REVERT: B 1205 GLN cc_start: 0.7566 (mm-40) cc_final: 0.7218 (mm110) REVERT: A 242 SER cc_start: 0.7325 (t) cc_final: 0.7088 (m) REVERT: A 346 PHE cc_start: 0.7718 (t80) cc_final: 0.7487 (t80) REVERT: A 485 GLU cc_start: 0.8456 (mm-30) cc_final: 0.8119 (mm-30) REVERT: A 492 GLU cc_start: 0.7055 (tm-30) cc_final: 0.5710 (mt-10) REVERT: A 543 CYS cc_start: 0.7322 (t) cc_final: 0.6673 (m) REVERT: A 762 THR cc_start: 0.7970 (m) cc_final: 0.7691 (p) REVERT: A 834 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6873 (mp0) REVERT: A 868 GLN cc_start: 0.8363 (tp-100) cc_final: 0.8122 (tp40) REVERT: A 889 LYS cc_start: 0.8172 (tttp) cc_final: 0.7864 (tttp) REVERT: A 1205 GLN cc_start: 0.7569 (mm-40) cc_final: 0.7247 (mm-40) outliers start: 43 outliers final: 25 residues processed: 272 average time/residue: 0.9177 time to fit residues: 279.8803 Evaluate side-chains 241 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 214 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 712 ASN Chi-restraints excluded: chain B residue 799 ASN Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain B residue 861 ASP Chi-restraints excluded: chain B residue 1028 TRP Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 834 GLU Chi-restraints excluded: chain A residue 861 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 8.9990 chunk 49 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 158 optimal weight: 0.7980 chunk 171 optimal weight: 1.9990 chunk 140 optimal weight: 0.0970 chunk 156 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 126 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 515 GLN B 731 ASN ** B 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 GLN A 731 ASN ** A 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12954 Z= 0.208 Angle : 0.602 9.746 17664 Z= 0.312 Chirality : 0.043 0.142 2062 Planarity : 0.004 0.049 2216 Dihedral : 4.808 19.628 1880 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 3.55 % Allowed : 15.37 % Favored : 81.08 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.21), residues: 1730 helix: 1.24 (0.17), residues: 964 sheet: 0.14 (0.58), residues: 92 loop : -2.14 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B1028 HIS 0.004 0.001 HIS A 773 PHE 0.027 0.001 PHE A 608 TYR 0.014 0.001 TYR B 353 ARG 0.008 0.000 ARG B1069 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 238 time to evaluate : 1.476 Fit side-chains REVERT: B 242 SER cc_start: 0.7314 (t) cc_final: 0.7058 (m) REVERT: B 311 ILE cc_start: 0.7828 (OUTLIER) cc_final: 0.7520 (mt) REVERT: B 346 PHE cc_start: 0.7808 (t80) cc_final: 0.7558 (t80) REVERT: B 469 LYS cc_start: 0.7379 (mmpt) cc_final: 0.7110 (mmmt) REVERT: B 492 GLU cc_start: 0.7031 (tm-30) cc_final: 0.5677 (mt-10) REVERT: B 543 CYS cc_start: 0.7263 (t) cc_final: 0.6745 (m) REVERT: B 713 MET cc_start: 0.7419 (OUTLIER) cc_final: 0.7005 (ttm) REVERT: B 762 THR cc_start: 0.7958 (m) cc_final: 0.7667 (p) REVERT: B 834 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6891 (mp0) REVERT: B 889 LYS cc_start: 0.8239 (tttp) cc_final: 0.7942 (tttp) REVERT: B 1095 LYS cc_start: 0.8479 (tmtt) cc_final: 0.8221 (tmtt) REVERT: B 1205 GLN cc_start: 0.7301 (mm-40) cc_final: 0.7060 (mm-40) REVERT: A 242 SER cc_start: 0.7313 (t) cc_final: 0.7050 (m) REVERT: A 288 ILE cc_start: 0.8067 (OUTLIER) cc_final: 0.7386 (pt) REVERT: A 346 PHE cc_start: 0.7807 (t80) cc_final: 0.7556 (t80) REVERT: A 469 LYS cc_start: 0.7333 (mmpt) cc_final: 0.7013 (mmmt) REVERT: A 485 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8023 (mm-30) REVERT: A 492 GLU cc_start: 0.7026 (tm-30) cc_final: 0.5662 (mt-10) REVERT: A 543 CYS cc_start: 0.7265 (t) cc_final: 0.6735 (m) REVERT: A 595 MET cc_start: 0.7739 (pp-130) cc_final: 0.7531 (ppp) REVERT: A 713 MET cc_start: 0.7416 (OUTLIER) cc_final: 0.6911 (ttm) REVERT: A 762 THR cc_start: 0.7940 (m) cc_final: 0.7653 (p) REVERT: A 834 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6854 (mp0) REVERT: A 868 GLN cc_start: 0.8350 (tp-100) cc_final: 0.8149 (tp40) REVERT: A 889 LYS cc_start: 0.8241 (tttp) cc_final: 0.7947 (tttp) REVERT: A 1095 LYS cc_start: 0.8497 (tmtt) cc_final: 0.8225 (tmtt) outliers start: 42 outliers final: 17 residues processed: 261 average time/residue: 0.8617 time to fit residues: 252.8415 Evaluate side-chains 244 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 221 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 712 ASN Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain B residue 1028 TRP Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 834 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 2.9990 chunk 119 optimal weight: 10.0000 chunk 82 optimal weight: 0.8980 chunk 17 optimal weight: 7.9990 chunk 75 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 158 optimal weight: 6.9990 chunk 168 optimal weight: 0.6980 chunk 150 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 ASN ** B 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN ** A 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12954 Z= 0.261 Angle : 0.621 10.059 17664 Z= 0.321 Chirality : 0.046 0.431 2062 Planarity : 0.004 0.042 2216 Dihedral : 4.791 19.634 1880 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 4.90 % Allowed : 16.64 % Favored : 78.46 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.20), residues: 1730 helix: 1.19 (0.17), residues: 978 sheet: -0.13 (0.56), residues: 98 loop : -2.19 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B1028 HIS 0.005 0.001 HIS B 822 PHE 0.021 0.002 PHE A 608 TYR 0.012 0.001 TYR A 353 ARG 0.007 0.001 ARG A1069 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 232 time to evaluate : 1.318 Fit side-chains REVERT: B 218 MET cc_start: 0.4039 (tpt) cc_final: 0.3774 (tpt) REVERT: B 242 SER cc_start: 0.7398 (t) cc_final: 0.7148 (m) REVERT: B 492 GLU cc_start: 0.7209 (tm-30) cc_final: 0.5785 (mt-10) REVERT: B 543 CYS cc_start: 0.7250 (t) cc_final: 0.6671 (m) REVERT: B 713 MET cc_start: 0.7540 (OUTLIER) cc_final: 0.7026 (ttm) REVERT: B 752 LYS cc_start: 0.6470 (tptt) cc_final: 0.6200 (tttp) REVERT: B 762 THR cc_start: 0.8069 (m) cc_final: 0.7649 (p) REVERT: B 790 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.8231 (mt0) REVERT: B 834 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6931 (mp0) REVERT: B 889 LYS cc_start: 0.8029 (tttp) cc_final: 0.7701 (tttp) REVERT: A 218 MET cc_start: 0.4134 (tpt) cc_final: 0.3872 (tpt) REVERT: A 242 SER cc_start: 0.7395 (t) cc_final: 0.7156 (m) REVERT: A 346 PHE cc_start: 0.7963 (t80) cc_final: 0.7719 (t80) REVERT: A 485 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7928 (mm-30) REVERT: A 492 GLU cc_start: 0.7203 (tm-30) cc_final: 0.5778 (mt-10) REVERT: A 543 CYS cc_start: 0.7207 (t) cc_final: 0.6574 (m) REVERT: A 713 MET cc_start: 0.7535 (OUTLIER) cc_final: 0.7022 (ttm) REVERT: A 752 LYS cc_start: 0.6466 (tptt) cc_final: 0.6193 (tttp) REVERT: A 762 THR cc_start: 0.8075 (m) cc_final: 0.7660 (p) REVERT: A 790 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8258 (mt0) REVERT: A 834 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6940 (mp0) REVERT: A 889 LYS cc_start: 0.8045 (tttp) cc_final: 0.7720 (tttp) REVERT: A 1095 LYS cc_start: 0.8490 (tmtt) cc_final: 0.8253 (tmtt) REVERT: A 1205 GLN cc_start: 0.7451 (mm110) cc_final: 0.7016 (mm-40) outliers start: 58 outliers final: 37 residues processed: 266 average time/residue: 0.8734 time to fit residues: 261.0066 Evaluate side-chains 260 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 217 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 710 TYR Chi-restraints excluded: chain B residue 712 ASN Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain B residue 790 GLN Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain B residue 861 ASP Chi-restraints excluded: chain B residue 1028 TRP Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 710 TYR Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 790 GLN Chi-restraints excluded: chain A residue 834 GLU Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 1028 TRP Chi-restraints excluded: chain A residue 1101 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 125 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 143 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 chunk 150 optimal weight: 0.0170 chunk 42 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 ASN ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12954 Z= 0.195 Angle : 0.576 9.647 17664 Z= 0.299 Chirality : 0.043 0.331 2062 Planarity : 0.004 0.041 2216 Dihedral : 4.566 18.616 1880 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 4.65 % Allowed : 17.65 % Favored : 77.70 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.20), residues: 1730 helix: 1.32 (0.17), residues: 976 sheet: -0.10 (0.55), residues: 98 loop : -2.17 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B1028 HIS 0.004 0.001 HIS B 859 PHE 0.017 0.001 PHE B 608 TYR 0.016 0.001 TYR B 746 ARG 0.006 0.000 ARG A1069 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 224 time to evaluate : 1.324 Fit side-chains REVERT: B 242 SER cc_start: 0.7472 (t) cc_final: 0.7129 (m) REVERT: B 492 GLU cc_start: 0.7191 (tm-30) cc_final: 0.5727 (mt-10) REVERT: B 543 CYS cc_start: 0.7396 (t) cc_final: 0.6672 (m) REVERT: B 713 MET cc_start: 0.7463 (OUTLIER) cc_final: 0.7056 (ttm) REVERT: B 752 LYS cc_start: 0.6474 (tptt) cc_final: 0.6218 (tttp) REVERT: B 762 THR cc_start: 0.8050 (m) cc_final: 0.7676 (p) REVERT: B 772 GLN cc_start: 0.7163 (mm-40) cc_final: 0.6783 (mt0) REVERT: B 834 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.6750 (mp0) REVERT: B 889 LYS cc_start: 0.7901 (tttp) cc_final: 0.7598 (tttp) REVERT: A 242 SER cc_start: 0.7353 (t) cc_final: 0.7115 (m) REVERT: A 311 ILE cc_start: 0.7706 (OUTLIER) cc_final: 0.7262 (mt) REVERT: A 384 VAL cc_start: 0.8144 (OUTLIER) cc_final: 0.7935 (p) REVERT: A 469 LYS cc_start: 0.7478 (mmpt) cc_final: 0.7247 (mmmt) REVERT: A 485 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7898 (mm-30) REVERT: A 492 GLU cc_start: 0.7186 (tm-30) cc_final: 0.5708 (mt-10) REVERT: A 543 CYS cc_start: 0.7400 (t) cc_final: 0.6666 (m) REVERT: A 713 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.7045 (ttm) REVERT: A 752 LYS cc_start: 0.6470 (tptt) cc_final: 0.6210 (tttp) REVERT: A 762 THR cc_start: 0.8039 (m) cc_final: 0.7656 (p) REVERT: A 772 GLN cc_start: 0.7141 (mm-40) cc_final: 0.6770 (mt0) REVERT: A 834 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.6759 (mp0) REVERT: A 1095 LYS cc_start: 0.8502 (tmtt) cc_final: 0.8209 (tmtt) outliers start: 55 outliers final: 31 residues processed: 258 average time/residue: 0.8475 time to fit residues: 246.3304 Evaluate side-chains 242 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 205 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 710 TYR Chi-restraints excluded: chain B residue 712 ASN Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain B residue 799 ASN Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain B residue 1028 TRP Chi-restraints excluded: chain B residue 1029 LEU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 710 TYR Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 834 GLU Chi-restraints excluded: chain A residue 1029 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 168 optimal weight: 0.4980 chunk 139 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 chunk 162 optimal weight: 7.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 680 ASN B 731 ASN B 790 GLN ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 680 ASN A 731 ASN A 790 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12954 Z= 0.227 Angle : 0.599 9.551 17664 Z= 0.309 Chirality : 0.043 0.195 2062 Planarity : 0.004 0.043 2216 Dihedral : 4.557 19.878 1880 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 5.32 % Allowed : 18.58 % Favored : 76.10 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.21), residues: 1730 helix: 1.37 (0.17), residues: 962 sheet: -0.08 (0.56), residues: 98 loop : -2.09 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B1028 HIS 0.004 0.001 HIS A 822 PHE 0.016 0.001 PHE A 608 TYR 0.013 0.001 TYR A 353 ARG 0.006 0.000 ARG B1069 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 214 time to evaluate : 1.354 Fit side-chains REVERT: B 242 SER cc_start: 0.7461 (t) cc_final: 0.7113 (m) REVERT: B 311 ILE cc_start: 0.7741 (OUTLIER) cc_final: 0.7303 (mt) REVERT: B 468 TYR cc_start: 0.7743 (m-80) cc_final: 0.7235 (m-80) REVERT: B 492 GLU cc_start: 0.7052 (tm-30) cc_final: 0.5584 (mt-10) REVERT: B 543 CYS cc_start: 0.7503 (t) cc_final: 0.6690 (m) REVERT: B 713 MET cc_start: 0.7622 (OUTLIER) cc_final: 0.7101 (ttm) REVERT: B 752 LYS cc_start: 0.6449 (tptt) cc_final: 0.6198 (tttp) REVERT: B 762 THR cc_start: 0.8027 (m) cc_final: 0.7628 (p) REVERT: B 772 GLN cc_start: 0.7158 (mm-40) cc_final: 0.6788 (mt0) REVERT: B 834 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.6800 (mp0) REVERT: A 242 SER cc_start: 0.7457 (t) cc_final: 0.7116 (m) REVERT: A 311 ILE cc_start: 0.7726 (OUTLIER) cc_final: 0.7278 (mt) REVERT: A 384 VAL cc_start: 0.8166 (OUTLIER) cc_final: 0.7954 (p) REVERT: A 468 TYR cc_start: 0.7791 (m-80) cc_final: 0.7336 (m-80) REVERT: A 469 LYS cc_start: 0.7413 (mmpt) cc_final: 0.7199 (mmmt) REVERT: A 485 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7886 (mm-30) REVERT: A 492 GLU cc_start: 0.7048 (tm-30) cc_final: 0.5576 (mt-10) REVERT: A 543 CYS cc_start: 0.7496 (t) cc_final: 0.6680 (m) REVERT: A 713 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.7090 (ttm) REVERT: A 752 LYS cc_start: 0.6441 (tptt) cc_final: 0.6189 (tttp) REVERT: A 762 THR cc_start: 0.8030 (m) cc_final: 0.7634 (p) REVERT: A 772 GLN cc_start: 0.7119 (mm-40) cc_final: 0.6768 (mt0) REVERT: A 834 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.6811 (mp0) REVERT: A 1095 LYS cc_start: 0.8500 (tmtt) cc_final: 0.8220 (tmtt) REVERT: A 1154 GLU cc_start: 0.7126 (mm-30) cc_final: 0.6921 (tp30) outliers start: 63 outliers final: 37 residues processed: 254 average time/residue: 0.8078 time to fit residues: 232.3171 Evaluate side-chains 244 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 200 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 710 TYR Chi-restraints excluded: chain B residue 712 ASN Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain B residue 799 ASN Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain B residue 861 ASP Chi-restraints excluded: chain B residue 1028 TRP Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 710 TYR Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 834 GLU Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1052 CYS Chi-restraints excluded: chain A residue 1165 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 141 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 167 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 102 optimal weight: 30.0000 chunk 77 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 ASN ** B 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1153 ASN ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN ** A 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1153 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 12954 Z= 0.393 Angle : 0.692 10.450 17664 Z= 0.356 Chirality : 0.048 0.228 2062 Planarity : 0.005 0.044 2216 Dihedral : 5.010 21.300 1880 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 5.57 % Allowed : 19.09 % Favored : 75.34 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.21), residues: 1730 helix: 1.10 (0.17), residues: 978 sheet: -0.45 (0.56), residues: 100 loop : -2.08 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B1028 HIS 0.008 0.002 HIS A 822 PHE 0.020 0.002 PHE A 907 TYR 0.017 0.002 TYR B 227 ARG 0.010 0.001 ARG B1069 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 205 time to evaluate : 1.293 Fit side-chains REVERT: B 242 SER cc_start: 0.7446 (t) cc_final: 0.7099 (m) REVERT: B 384 VAL cc_start: 0.8102 (OUTLIER) cc_final: 0.7892 (p) REVERT: B 492 GLU cc_start: 0.7136 (tm-30) cc_final: 0.5765 (mt-10) REVERT: B 713 MET cc_start: 0.7777 (OUTLIER) cc_final: 0.7213 (ttm) REVERT: B 752 LYS cc_start: 0.6557 (tptt) cc_final: 0.6305 (tttp) REVERT: B 762 THR cc_start: 0.8142 (m) cc_final: 0.7679 (p) REVERT: B 834 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.6757 (mp0) REVERT: A 242 SER cc_start: 0.7443 (t) cc_final: 0.7108 (m) REVERT: A 384 VAL cc_start: 0.8101 (OUTLIER) cc_final: 0.7889 (p) REVERT: A 485 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7832 (mm-30) REVERT: A 492 GLU cc_start: 0.7139 (tm-30) cc_final: 0.5751 (mt-10) REVERT: A 713 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7205 (ttm) REVERT: A 752 LYS cc_start: 0.6549 (tptt) cc_final: 0.6296 (tttp) REVERT: A 762 THR cc_start: 0.8133 (m) cc_final: 0.7670 (p) REVERT: A 834 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.6762 (mp0) outliers start: 66 outliers final: 41 residues processed: 249 average time/residue: 0.7743 time to fit residues: 219.4100 Evaluate side-chains 232 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 185 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 599 PHE Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 710 TYR Chi-restraints excluded: chain B residue 712 ASN Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 799 ASN Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain B residue 861 ASP Chi-restraints excluded: chain B residue 1028 TRP Chi-restraints excluded: chain B residue 1052 CYS Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 599 PHE Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 710 TYR Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 834 GLU Chi-restraints excluded: chain A residue 1052 CYS Chi-restraints excluded: chain A residue 1165 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 32 optimal weight: 20.0000 chunk 106 optimal weight: 1.9990 chunk 114 optimal weight: 0.3980 chunk 82 optimal weight: 0.5980 chunk 15 optimal weight: 30.0000 chunk 131 optimal weight: 0.9990 chunk 152 optimal weight: 0.9990 chunk 160 optimal weight: 2.9990 chunk 146 optimal weight: 0.7980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 ASN B1153 ASN ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN A1153 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12954 Z= 0.199 Angle : 0.596 9.196 17664 Z= 0.306 Chirality : 0.043 0.191 2062 Planarity : 0.004 0.044 2216 Dihedral : 4.600 19.915 1880 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 4.22 % Allowed : 21.45 % Favored : 74.32 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.21), residues: 1730 helix: 1.34 (0.17), residues: 964 sheet: -0.30 (0.56), residues: 98 loop : -2.05 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B1028 HIS 0.005 0.001 HIS B 859 PHE 0.015 0.001 PHE B1210 TYR 0.017 0.001 TYR B 746 ARG 0.009 0.000 ARG B1069 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 201 time to evaluate : 1.441 Fit side-chains REVERT: B 242 SER cc_start: 0.7582 (t) cc_final: 0.7075 (m) REVERT: B 384 VAL cc_start: 0.8098 (OUTLIER) cc_final: 0.7878 (p) REVERT: B 419 ILE cc_start: 0.7599 (mm) cc_final: 0.7334 (mt) REVERT: B 468 TYR cc_start: 0.7763 (m-80) cc_final: 0.6968 (m-80) REVERT: B 492 GLU cc_start: 0.7120 (tm-30) cc_final: 0.5678 (mt-10) REVERT: B 543 CYS cc_start: 0.7501 (t) cc_final: 0.6351 (m) REVERT: B 713 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.7058 (ttm) REVERT: B 752 LYS cc_start: 0.6546 (tptt) cc_final: 0.6300 (tttp) REVERT: B 762 THR cc_start: 0.7942 (m) cc_final: 0.7551 (p) REVERT: B 772 GLN cc_start: 0.7126 (mm-40) cc_final: 0.6761 (mt0) REVERT: B 834 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7221 (mm-30) REVERT: A 242 SER cc_start: 0.7581 (t) cc_final: 0.7084 (m) REVERT: A 384 VAL cc_start: 0.8143 (OUTLIER) cc_final: 0.7924 (p) REVERT: A 468 TYR cc_start: 0.7602 (m-80) cc_final: 0.6820 (m-80) REVERT: A 492 GLU cc_start: 0.7059 (tm-30) cc_final: 0.5579 (mt-10) REVERT: A 543 CYS cc_start: 0.7509 (t) cc_final: 0.6340 (m) REVERT: A 713 MET cc_start: 0.7553 (OUTLIER) cc_final: 0.7057 (ttm) REVERT: A 752 LYS cc_start: 0.6541 (tptt) cc_final: 0.6294 (tttp) REVERT: A 762 THR cc_start: 0.7963 (m) cc_final: 0.7573 (p) REVERT: A 772 GLN cc_start: 0.7174 (mm-40) cc_final: 0.6816 (mt0) REVERT: A 834 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7229 (mm-30) outliers start: 50 outliers final: 36 residues processed: 232 average time/residue: 0.7997 time to fit residues: 210.9764 Evaluate side-chains 241 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 199 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 599 PHE Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 710 TYR Chi-restraints excluded: chain B residue 712 ASN Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain B residue 728 PHE Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 799 ASN Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain B residue 861 ASP Chi-restraints excluded: chain B residue 1028 TRP Chi-restraints excluded: chain B residue 1193 ASP Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 599 PHE Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 710 TYR Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 834 GLU Chi-restraints excluded: chain A residue 1165 ILE Chi-restraints excluded: chain A residue 1193 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 0.7980 chunk 160 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 68 optimal weight: 0.2980 chunk 122 optimal weight: 9.9990 chunk 47 optimal weight: 0.9990 chunk 141 optimal weight: 0.0050 chunk 147 optimal weight: 2.9990 chunk 155 optimal weight: 0.5980 chunk 102 optimal weight: 30.0000 chunk 165 optimal weight: 5.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 ASN ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12954 Z= 0.179 Angle : 0.572 9.248 17664 Z= 0.294 Chirality : 0.042 0.182 2062 Planarity : 0.004 0.044 2216 Dihedral : 4.339 19.518 1880 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 3.72 % Allowed : 21.96 % Favored : 74.32 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.21), residues: 1730 helix: 1.48 (0.17), residues: 960 sheet: -0.14 (0.56), residues: 98 loop : -1.97 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B1028 HIS 0.004 0.001 HIS B 859 PHE 0.013 0.001 PHE B 608 TYR 0.016 0.001 TYR B 746 ARG 0.008 0.000 ARG A1069 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 211 time to evaluate : 1.499 Fit side-chains REVERT: B 242 SER cc_start: 0.7722 (t) cc_final: 0.7212 (m) REVERT: B 419 ILE cc_start: 0.7569 (mm) cc_final: 0.7302 (mt) REVERT: B 468 TYR cc_start: 0.7746 (m-80) cc_final: 0.6969 (m-80) REVERT: B 485 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7794 (mm-30) REVERT: B 492 GLU cc_start: 0.6952 (tm-30) cc_final: 0.5460 (mt-10) REVERT: B 543 CYS cc_start: 0.7439 (t) cc_final: 0.6351 (m) REVERT: B 713 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.6921 (ttm) REVERT: B 752 LYS cc_start: 0.6559 (tptt) cc_final: 0.6339 (tttp) REVERT: B 762 THR cc_start: 0.7960 (m) cc_final: 0.7593 (p) REVERT: B 772 GLN cc_start: 0.7124 (mm-40) cc_final: 0.6785 (mt0) REVERT: B 799 ASN cc_start: 0.7894 (OUTLIER) cc_final: 0.7474 (p0) REVERT: B 834 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7166 (mm-30) REVERT: B 865 GLU cc_start: 0.7639 (pt0) cc_final: 0.7371 (pt0) REVERT: B 1154 GLU cc_start: 0.6979 (mm-30) cc_final: 0.6623 (tp30) REVERT: A 242 SER cc_start: 0.7723 (t) cc_final: 0.7217 (m) REVERT: A 384 VAL cc_start: 0.8112 (OUTLIER) cc_final: 0.7906 (p) REVERT: A 468 TYR cc_start: 0.7782 (m-80) cc_final: 0.7014 (m-80) REVERT: A 492 GLU cc_start: 0.6948 (tm-30) cc_final: 0.5463 (mt-10) REVERT: A 543 CYS cc_start: 0.7441 (t) cc_final: 0.6333 (m) REVERT: A 713 MET cc_start: 0.7443 (OUTLIER) cc_final: 0.6931 (ttm) REVERT: A 752 LYS cc_start: 0.6555 (tptt) cc_final: 0.6332 (tttp) REVERT: A 762 THR cc_start: 0.7948 (m) cc_final: 0.7579 (p) REVERT: A 772 GLN cc_start: 0.7085 (mm-40) cc_final: 0.6778 (mt0) REVERT: A 834 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7170 (mm-30) REVERT: A 1095 LYS cc_start: 0.8529 (tmtt) cc_final: 0.8234 (tmtt) REVERT: A 1154 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6809 (tp30) outliers start: 44 outliers final: 29 residues processed: 240 average time/residue: 0.8611 time to fit residues: 233.3380 Evaluate side-chains 240 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 205 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 599 PHE Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 710 TYR Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 799 ASN Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain B residue 1028 TRP Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 599 PHE Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 710 TYR Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 834 GLU Chi-restraints excluded: chain A residue 1165 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 chunk 114 optimal weight: 0.0010 chunk 173 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 109 optimal weight: 9.9990 chunk 147 optimal weight: 0.5980 overall best weight: 1.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 ASN B1203 ASN ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN A1203 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12954 Z= 0.229 Angle : 0.605 10.693 17664 Z= 0.307 Chirality : 0.043 0.184 2062 Planarity : 0.004 0.044 2216 Dihedral : 4.459 22.800 1880 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 3.55 % Allowed : 22.21 % Favored : 74.24 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.21), residues: 1730 helix: 1.35 (0.17), residues: 978 sheet: -0.20 (0.56), residues: 98 loop : -1.93 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B1028 HIS 0.005 0.001 HIS A 822 PHE 0.015 0.001 PHE A 811 TYR 0.018 0.001 TYR A 746 ARG 0.008 0.001 ARG A1069 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 202 time to evaluate : 1.292 Fit side-chains REVERT: B 242 SER cc_start: 0.7738 (t) cc_final: 0.7221 (m) REVERT: B 384 VAL cc_start: 0.8123 (OUTLIER) cc_final: 0.7895 (p) REVERT: B 419 ILE cc_start: 0.7610 (mm) cc_final: 0.7349 (mt) REVERT: B 468 TYR cc_start: 0.7733 (m-80) cc_final: 0.6975 (m-80) REVERT: B 492 GLU cc_start: 0.6991 (tm-30) cc_final: 0.5501 (mt-10) REVERT: B 543 CYS cc_start: 0.7477 (t) cc_final: 0.6384 (m) REVERT: B 607 ILE cc_start: 0.6523 (mt) cc_final: 0.6302 (mp) REVERT: B 713 MET cc_start: 0.7575 (OUTLIER) cc_final: 0.7021 (ttm) REVERT: B 752 LYS cc_start: 0.6594 (tptt) cc_final: 0.6377 (tttp) REVERT: B 762 THR cc_start: 0.8034 (m) cc_final: 0.7634 (p) REVERT: B 772 GLN cc_start: 0.7201 (mm-40) cc_final: 0.6830 (mt0) REVERT: B 834 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7185 (mm-30) REVERT: B 1154 GLU cc_start: 0.7054 (mm-30) cc_final: 0.6803 (tp30) REVERT: A 242 SER cc_start: 0.7738 (t) cc_final: 0.7223 (m) REVERT: A 384 VAL cc_start: 0.8106 (OUTLIER) cc_final: 0.7897 (p) REVERT: A 468 TYR cc_start: 0.7800 (m-80) cc_final: 0.7023 (m-80) REVERT: A 492 GLU cc_start: 0.7008 (tm-30) cc_final: 0.5503 (mt-10) REVERT: A 543 CYS cc_start: 0.7475 (t) cc_final: 0.6375 (m) REVERT: A 713 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.7021 (ttm) REVERT: A 752 LYS cc_start: 0.6589 (tptt) cc_final: 0.6370 (tttp) REVERT: A 762 THR cc_start: 0.8024 (m) cc_final: 0.7623 (p) REVERT: A 772 GLN cc_start: 0.7217 (mm-40) cc_final: 0.6861 (mt0) REVERT: A 834 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7189 (mm-30) REVERT: A 1095 LYS cc_start: 0.8536 (tmtt) cc_final: 0.8243 (tmtt) outliers start: 42 outliers final: 31 residues processed: 233 average time/residue: 0.8112 time to fit residues: 213.9456 Evaluate side-chains 238 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 201 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 599 PHE Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 710 TYR Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 799 ASN Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain B residue 1028 TRP Chi-restraints excluded: chain B residue 1203 ASN Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 599 PHE Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 710 TYR Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 834 GLU Chi-restraints excluded: chain A residue 1165 ILE Chi-restraints excluded: chain A residue 1203 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 42 optimal weight: 0.9990 chunk 127 optimal weight: 0.7980 chunk 20 optimal weight: 7.9990 chunk 38 optimal weight: 0.1980 chunk 138 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 ASN ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.167374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.134527 restraints weight = 15462.689| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.87 r_work: 0.3505 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 12954 Z= 0.251 Angle : 0.996 59.195 17664 Z= 0.586 Chirality : 0.046 0.527 2062 Planarity : 0.006 0.147 2216 Dihedral : 4.532 22.691 1880 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.21 % Favored : 91.73 % Rotamer: Outliers : 3.72 % Allowed : 21.71 % Favored : 74.58 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.21), residues: 1730 helix: 1.35 (0.17), residues: 978 sheet: -0.20 (0.56), residues: 98 loop : -1.97 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B1028 HIS 0.013 0.002 HIS B1204 PHE 0.015 0.001 PHE A 811 TYR 0.017 0.001 TYR A 746 ARG 0.008 0.000 ARG B1069 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4613.24 seconds wall clock time: 82 minutes 44.10 seconds (4964.10 seconds total)