Starting phenix.real_space_refine on Thu Feb 15 00:37:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7myo_24082/02_2024/7myo_24082_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7myo_24082/02_2024/7myo_24082.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7myo_24082/02_2024/7myo_24082.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7myo_24082/02_2024/7myo_24082.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7myo_24082/02_2024/7myo_24082_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7myo_24082/02_2024/7myo_24082_updated.pdb" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 77 5.16 5 C 6763 2.51 5 N 1848 2.21 5 O 1943 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 330": "OD1" <-> "OD2" Residue "B GLU 469": "OE1" <-> "OE2" Residue "B GLU 546": "OE1" <-> "OE2" Residue "A PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 939": "OD1" <-> "OD2" Residue "A PHE 977": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1002": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1045": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10634 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 2412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2412 Classifications: {'peptide': 286} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 281} Chain: "A" Number of atoms: 8222 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 993, 8137 Unusual residues: {'1LT': 1} Classifications: {'peptide': 992, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 945, None: 1} Not linked: pdbres="GLY A1050 " pdbres="1LT A1101 " Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 993, 8137 Unusual residues: {'1LT': 1} Classifications: {'peptide': 992, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 945, None: 1} Not linked: pdbres="GLY A1050 " pdbres="1LT A1101 " Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 8225 Residues with excluded nonbonded symmetry interactions: 9 residue: pdb=" N AARG A 617 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 617 " occ=0.50 residue: pdb=" N ALYS A 621 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 621 " occ=0.50 residue: pdb=" N AARG A 662 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 662 " occ=0.50 residue: pdb=" N AARG A 899 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 899 " occ=0.50 residue: pdb=" N AARG A 951 " occ=0.63 ... (20 atoms not shown) pdb=" NH2BARG A 951 " occ=0.37 residue: pdb=" N AVAL A 952 " occ=0.63 ... (12 atoms not shown) pdb=" CG2BVAL A 952 " occ=0.37 residue: pdb=" N APRO A 953 " occ=0.63 ... (12 atoms not shown) pdb=" CD BPRO A 953 " occ=0.37 residue: pdb=" N APHE A 954 " occ=0.63 ... (20 atoms not shown) pdb=" CZ BPHE A 954 " occ=0.37 residue: pdb=" N AVAL A 955 " occ=0.63 ... (12 atoms not shown) pdb=" CG2BVAL A 955 " occ=0.37 Time building chain proxies: 9.59, per 1000 atoms: 0.90 Number of scatterers: 10634 At special positions: 0 Unit cell: (89.87, 108.68, 135.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 77 16.00 F 3 9.00 O 1943 8.00 N 1848 7.00 C 6763 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 4.40 Conformation dependent library (CDL) restraints added in 3.4 seconds 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2466 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 7 sheets defined 44.9% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.41 Creating SS restraints... Processing helix chain 'B' and resid 340 through 347 Processing helix chain 'B' and resid 386 through 388 No H-bonds generated for 'chain 'B' and resid 386 through 388' Processing helix chain 'B' and resid 401 through 410 Processing helix chain 'B' and resid 433 through 435 No H-bonds generated for 'chain 'B' and resid 433 through 435' Processing helix chain 'B' and resid 442 through 507 removed outlier: 4.909A pdb=" N GLU B 507 " --> pdb=" O ARG B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 514 Processing helix chain 'B' and resid 519 through 587 removed outlier: 3.927A pdb=" N LEU B 531 " --> pdb=" O ASN B 527 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS B 532 " --> pdb=" O TYR B 528 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP B 548 " --> pdb=" O ARG B 544 " (cutoff:3.500A) Proline residue: B 568 - end of helix Processing helix chain 'B' and resid 594 through 598 removed outlier: 3.673A pdb=" N LEU B 598 " --> pdb=" O LEU B 594 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 594 through 598' Processing helix chain 'A' and resid 42 through 55 removed outlier: 3.605A pdb=" N HIS A 47 " --> pdb=" O ILE A 43 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLU A 48 " --> pdb=" O THR A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 121 Processing helix chain 'A' and resid 125 through 130 Processing helix chain 'A' and resid 134 through 154 removed outlier: 4.196A pdb=" N LEU A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASN A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL A 146 " --> pdb=" O ASN A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 166 Processing helix chain 'A' and resid 179 through 182 No H-bonds generated for 'chain 'A' and resid 179 through 182' Processing helix chain 'A' and resid 217 through 228 Processing helix chain 'A' and resid 241 through 247 Processing helix chain 'A' and resid 271 through 279 Processing helix chain 'A' and resid 290 through 296 Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 327 through 329 No H-bonds generated for 'chain 'A' and resid 327 through 329' Processing helix chain 'A' and resid 393 through 395 No H-bonds generated for 'chain 'A' and resid 393 through 395' Processing helix chain 'A' and resid 489 through 501 removed outlier: 3.548A pdb=" N VAL A 500 " --> pdb=" O ALA A 496 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER A 501 " --> pdb=" O ASN A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 535 Processing helix chain 'A' and resid 545 through 553 Processing helix chain 'A' and resid 563 through 570 Proline residue: A 566 - end of helix Processing helix chain 'A' and resid 578 through 589 removed outlier: 3.533A pdb=" N ASP A 589 " --> pdb=" O CYS A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 602 removed outlier: 4.452A pdb=" N GLU A 600 " --> pdb=" O GLU A 596 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU A 601 " --> pdb=" O GLN A 597 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N LEU A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 622 Processing helix chain 'A' and resid 625 through 630 Processing helix chain 'A' and resid 632 through 641 removed outlier: 3.902A pdb=" N LYS A 640 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TYR A 641 " --> pdb=" O GLN A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 658 Processing helix chain 'A' and resid 661 through 674 removed outlier: 3.923A pdb=" N GLU A 674 " --> pdb=" O HIS A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 694 Processing helix chain 'A' and resid 696 through 720 Processing helix chain 'A' and resid 733 through 740 Processing helix chain 'A' and resid 742 through 748 removed outlier: 3.935A pdb=" N ALA A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 748 " --> pdb=" O PHE A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 792 removed outlier: 4.438A pdb=" N GLU A 791 " --> pdb=" O ILE A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 827 Processing helix chain 'A' and resid 857 through 866 Processing helix chain 'A' and resid 876 through 884 Processing helix chain 'A' and resid 887 through 910 removed outlier: 4.448A pdb=" N ASP A 891 " --> pdb=" O GLU A 888 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER A 900 " --> pdb=" O PHE A 897 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N CYS A 905 " --> pdb=" O ALA A 902 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL A 906 " --> pdb=" O GLY A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 964 Processing helix chain 'A' and resid 975 through 1005 removed outlier: 3.987A pdb=" N ARG A 979 " --> pdb=" O ARG A 975 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N HIS A 994 " --> pdb=" O ALA A 990 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ASN A 996 " --> pdb=" O ARG A 992 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU A 997 " --> pdb=" O GLN A 993 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE A 998 " --> pdb=" O HIS A 994 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N MET A1005 " --> pdb=" O LEU A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1026 Processing helix chain 'A' and resid 1032 through 1044 Processing sheet with id= A, first strand: chain 'A' and resid 31 through 36 removed outlier: 3.615A pdb=" N VAL A 32 " --> pdb=" O CYS A 24 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N PHE A 98 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N VAL A 73 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N PHE A 70 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER A 72 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 207 through 212 removed outlier: 3.531A pdb=" N LYS A 253 " --> pdb=" O MET A 286 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 335 through 338 Processing sheet with id= D, first strand: chain 'A' and resid 353 through 355 removed outlier: 4.391A pdb=" N LYS A 353 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 409 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N SER A 408 " --> pdb=" O PRO A 421 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 440 through 444 Processing sheet with id= F, first strand: chain 'A' and resid 779 through 784 Processing sheet with id= G, first strand: chain 'A' and resid 854 through 856 425 hydrogen bonds defined for protein. 1130 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: 3.56 Time building geometry restraints manager: 4.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1774 1.32 - 1.44: 2816 1.44 - 1.56: 6146 1.56 - 1.69: 2 1.69 - 1.81: 121 Bond restraints: 10859 Sorted by residual: bond pdb=" C3 1LT A1101 " pdb=" N1 1LT A1101 " ideal model delta sigma weight residual 1.391 1.485 -0.094 2.00e-02 2.50e+03 2.23e+01 bond pdb=" C2 1LT A1101 " pdb=" N1 1LT A1101 " ideal model delta sigma weight residual 1.368 1.458 -0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C3 1LT A1101 " pdb=" N2 1LT A1101 " ideal model delta sigma weight residual 1.348 1.435 -0.087 2.00e-02 2.50e+03 1.87e+01 bond pdb=" N 1LT A1101 " pdb=" C1 1LT A1101 " ideal model delta sigma weight residual 1.368 1.445 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" C7 1LT A1101 " pdb=" N2 1LT A1101 " ideal model delta sigma weight residual 1.444 1.520 -0.076 2.00e-02 2.50e+03 1.43e+01 ... (remaining 10854 not shown) Histogram of bond angle deviations from ideal: 94.34 - 102.38: 54 102.38 - 110.43: 2476 110.43 - 118.47: 5952 118.47 - 126.52: 6006 126.52 - 134.56: 163 Bond angle restraints: 14651 Sorted by residual: angle pdb=" N ASP A1017 " pdb=" CA ASP A1017 " pdb=" C ASP A1017 " ideal model delta sigma weight residual 114.31 108.20 6.11 1.29e+00 6.01e-01 2.25e+01 angle pdb=" C ASP A 939 " pdb=" N HIS A 940 " pdb=" CA HIS A 940 " ideal model delta sigma weight residual 121.54 129.94 -8.40 1.91e+00 2.74e-01 1.93e+01 angle pdb=" N GLU B 537 " pdb=" CA GLU B 537 " pdb=" CB GLU B 537 " ideal model delta sigma weight residual 110.30 117.00 -6.70 1.54e+00 4.22e-01 1.90e+01 angle pdb=" CB MET A1040 " pdb=" CG MET A1040 " pdb=" SD MET A1040 " ideal model delta sigma weight residual 112.70 125.56 -12.86 3.00e+00 1.11e-01 1.84e+01 angle pdb=" CG1 ILE A 211 " pdb=" CB ILE A 211 " pdb=" CG2 ILE A 211 " ideal model delta sigma weight residual 110.70 99.90 10.80 3.00e+00 1.11e-01 1.30e+01 ... (remaining 14646 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 5886 17.47 - 34.95: 618 34.95 - 52.42: 113 52.42 - 69.89: 32 69.89 - 87.36: 13 Dihedral angle restraints: 6662 sinusoidal: 2859 harmonic: 3803 Sorted by residual: dihedral pdb=" CA LEU A 209 " pdb=" C LEU A 209 " pdb=" N LYS A 210 " pdb=" CA LYS A 210 " ideal model delta harmonic sigma weight residual -180.00 -153.50 -26.50 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA PHE B 512 " pdb=" C PHE B 512 " pdb=" N LYS B 513 " pdb=" CA LYS B 513 " ideal model delta harmonic sigma weight residual 180.00 159.45 20.55 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA LEU A 262 " pdb=" C LEU A 262 " pdb=" N GLU A 263 " pdb=" CA GLU A 263 " ideal model delta harmonic sigma weight residual -180.00 -161.54 -18.46 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 6659 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1062 0.044 - 0.088: 374 0.088 - 0.132: 117 0.132 - 0.175: 19 0.175 - 0.219: 9 Chirality restraints: 1581 Sorted by residual: chirality pdb=" CB ILE A 921 " pdb=" CA ILE A 921 " pdb=" CG1 ILE A 921 " pdb=" CG2 ILE A 921 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ASN A 202 " pdb=" N ASN A 202 " pdb=" C ASN A 202 " pdb=" CB ASN A 202 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.93e-01 chirality pdb=" CG LEU A 267 " pdb=" CB LEU A 267 " pdb=" CD1 LEU A 267 " pdb=" CD2 LEU A 267 " both_signs ideal model delta sigma weight residual False -2.59 -2.79 0.20 2.00e-01 2.50e+01 9.71e-01 ... (remaining 1578 not shown) Planarity restraints: 1883 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 426 " 0.082 5.00e-02 4.00e+02 1.24e-01 2.44e+01 pdb=" N PRO B 427 " -0.214 5.00e-02 4.00e+02 pdb=" CA PRO B 427 " 0.067 5.00e-02 4.00e+02 pdb=" CD PRO B 427 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 177 " -0.076 5.00e-02 4.00e+02 1.15e-01 2.11e+01 pdb=" N PRO A 178 " 0.198 5.00e-02 4.00e+02 pdb=" CA PRO A 178 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO A 178 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 457 " -0.069 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO A 458 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO A 458 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 458 " -0.056 5.00e-02 4.00e+02 ... (remaining 1880 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1521 2.76 - 3.29: 10734 3.29 - 3.83: 18443 3.83 - 4.36: 21491 4.36 - 4.90: 35236 Nonbonded interactions: 87425 Sorted by model distance: nonbonded pdb=" O TYR A1038 " pdb=" OE1 GLN A1042 " model vdw 2.225 3.040 nonbonded pdb=" OH TYR A 988 " pdb=" O LEU A1026 " model vdw 2.247 2.440 nonbonded pdb=" OG SER A 499 " pdb=" OE1 GLN A 582 " model vdw 2.253 2.440 nonbonded pdb=" O ASP A 895 " pdb=" OG1 THR A 898 " model vdw 2.257 2.440 nonbonded pdb=" OE2 GLU B 332 " pdb=" OH TYR B 431 " model vdw 2.268 2.440 ... (remaining 87420 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.37 max=1.00 mean=0.99 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: 0.340 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: 0.030 Extract box with map and model: 2.220 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 37.220 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.180 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:13.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 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 0.094 10859 Z= 0.309 Angle : 0.894 12.856 14651 Z= 0.455 Chirality : 0.051 0.219 1581 Planarity : 0.008 0.124 1883 Dihedral : 15.195 87.363 4196 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.59 % Allowed : 0.85 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.22), residues: 1281 helix: -0.71 (0.19), residues: 593 sheet: -1.80 (0.43), residues: 137 loop : -1.73 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP B 335 HIS 0.017 0.001 HIS A 940 PHE 0.035 0.003 PHE A 937 TYR 0.031 0.002 TYR A 165 ARG 0.016 0.001 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 305 time to evaluate : 1.243 Fit side-chains revert: symmetry clash REVERT: A 526 ASN cc_start: 0.7934 (p0) cc_final: 0.7636 (p0) REVERT: A 988 TYR cc_start: 0.5782 (t80) cc_final: 0.5575 (t80) outliers start: 1 outliers final: 0 residues processed: 305 average time/residue: 1.1125 time to fit residues: 368.7037 Evaluate side-chains 211 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 53 optimal weight: 0.0020 chunk 32 optimal weight: 0.4980 chunk 64 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 38 optimal weight: 0.5980 chunk 60 optimal weight: 7.9990 chunk 74 optimal weight: 0.0170 chunk 115 optimal weight: 0.9980 overall best weight: 0.3826 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 HIS A 661 GLN A 701 HIS ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 GLN A 785 ASN ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10859 Z= 0.201 Angle : 0.704 11.590 14651 Z= 0.350 Chirality : 0.043 0.164 1581 Planarity : 0.006 0.085 1883 Dihedral : 5.915 59.339 1437 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.03 % Allowed : 18.29 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.22), residues: 1281 helix: -0.24 (0.20), residues: 602 sheet: -1.29 (0.46), residues: 121 loop : -1.75 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 333 HIS 0.010 0.001 HIS A 940 PHE 0.039 0.002 PHE A 667 TYR 0.020 0.001 TYR A 432 ARG 0.011 0.000 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 235 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.7558 (mpp) cc_final: 0.6573 (mpt) REVERT: A 391 ILE cc_start: 0.7477 (OUTLIER) cc_final: 0.7128 (tp) REVERT: A 807 LEU cc_start: 0.8133 (mp) cc_final: 0.7822 (mp) REVERT: A 839 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6764 (tt) REVERT: A 977 PHE cc_start: 0.8060 (t80) cc_final: 0.7812 (t80) REVERT: A 1000 ASN cc_start: 0.6477 (t0) cc_final: 0.6031 (m-40) REVERT: A 1037 GLU cc_start: 0.7264 (tm-30) cc_final: 0.6998 (tm-30) outliers start: 18 outliers final: 5 residues processed: 244 average time/residue: 0.9358 time to fit residues: 251.2664 Evaluate side-chains 216 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 209 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 993 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN A 59 HIS A 170 ASN A 202 ASN A 426 ASN ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 HIS ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 GLN ** A 917 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 10859 Z= 0.301 Angle : 0.750 10.433 14651 Z= 0.377 Chirality : 0.046 0.242 1581 Planarity : 0.006 0.075 1883 Dihedral : 5.481 52.740 1437 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 21.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.39 % Allowed : 20.75 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.23), residues: 1281 helix: -0.02 (0.21), residues: 606 sheet: -1.89 (0.43), residues: 141 loop : -1.61 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 780 HIS 0.011 0.001 HIS A 59 PHE 0.043 0.003 PHE A 667 TYR 0.023 0.002 TYR A 985 ARG 0.010 0.001 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 241 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 420 LEU cc_start: 0.6232 (OUTLIER) cc_final: 0.6031 (mm) REVERT: B 449 LEU cc_start: 0.5869 (OUTLIER) cc_final: 0.5667 (tm) REVERT: B 537 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7500 (pm20) REVERT: A 58 LEU cc_start: 0.6618 (OUTLIER) cc_final: 0.6275 (mm) REVERT: A 330 ILE cc_start: 0.5817 (mt) cc_final: 0.5562 (mt) REVERT: A 391 ILE cc_start: 0.7714 (OUTLIER) cc_final: 0.7350 (tp) REVERT: A 637 GLN cc_start: 0.7105 (OUTLIER) cc_final: 0.6609 (mp10) REVERT: A 698 TYR cc_start: 0.7265 (t80) cc_final: 0.6755 (t80) outliers start: 34 outliers final: 17 residues processed: 257 average time/residue: 0.9855 time to fit residues: 278.0915 Evaluate side-chains 242 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 219 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 417 ASN Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 637 GLN Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 993 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 60 optimal weight: 0.3980 chunk 109 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 HIS A 202 ASN ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 HIS ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 10859 Z= 0.236 Angle : 0.704 10.219 14651 Z= 0.350 Chirality : 0.044 0.278 1581 Planarity : 0.005 0.069 1883 Dihedral : 5.295 55.679 1437 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 20.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 3.64 % Allowed : 23.54 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.23), residues: 1281 helix: 0.11 (0.21), residues: 597 sheet: -1.63 (0.43), residues: 132 loop : -1.61 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 780 HIS 0.021 0.001 HIS A 59 PHE 0.045 0.002 PHE A 667 TYR 0.031 0.002 TYR A 988 ARG 0.013 0.001 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 232 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 413 LEU cc_start: 0.6604 (OUTLIER) cc_final: 0.6300 (mt) REVERT: B 420 LEU cc_start: 0.6326 (OUTLIER) cc_final: 0.5960 (mm) REVERT: B 537 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7505 (pm20) REVERT: A 123 MET cc_start: 0.5694 (OUTLIER) cc_final: 0.4919 (pp-130) REVERT: A 330 ILE cc_start: 0.5813 (mt) cc_final: 0.5521 (mt) REVERT: A 391 ILE cc_start: 0.7696 (OUTLIER) cc_final: 0.7335 (tp) REVERT: A 599 MET cc_start: 0.6993 (mtm) cc_final: 0.6669 (mtt) REVERT: A 637 GLN cc_start: 0.7028 (OUTLIER) cc_final: 0.6422 (mp10) REVERT: A 698 TYR cc_start: 0.7145 (t80) cc_final: 0.6747 (t80) outliers start: 37 outliers final: 17 residues processed: 252 average time/residue: 0.9674 time to fit residues: 268.1624 Evaluate side-chains 235 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 212 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 417 ASN Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 637 GLN Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 993 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 0.0570 chunk 69 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 91 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 overall best weight: 0.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 HIS A 202 ASN ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 HIS ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 917 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10859 Z= 0.223 Angle : 0.707 9.492 14651 Z= 0.350 Chirality : 0.044 0.200 1581 Planarity : 0.005 0.066 1883 Dihedral : 5.151 56.345 1437 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 19.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 3.64 % Allowed : 24.72 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.23), residues: 1281 helix: 0.16 (0.21), residues: 597 sheet: -1.57 (0.42), residues: 134 loop : -1.53 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 333 HIS 0.011 0.001 HIS A 59 PHE 0.044 0.002 PHE A 667 TYR 0.017 0.001 TYR A 988 ARG 0.010 0.001 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 224 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 326 MET cc_start: 0.4752 (OUTLIER) cc_final: 0.4528 (ptt) REVERT: B 403 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7588 (tp30) REVERT: B 413 LEU cc_start: 0.6527 (OUTLIER) cc_final: 0.6240 (mt) REVERT: B 420 LEU cc_start: 0.6314 (OUTLIER) cc_final: 0.5943 (mm) REVERT: B 537 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7521 (pm20) REVERT: A 123 MET cc_start: 0.5617 (OUTLIER) cc_final: 0.4822 (pp-130) REVERT: A 330 ILE cc_start: 0.5833 (mt) cc_final: 0.5592 (mt) REVERT: A 391 ILE cc_start: 0.7679 (OUTLIER) cc_final: 0.7311 (tp) REVERT: A 637 GLN cc_start: 0.6923 (OUTLIER) cc_final: 0.6353 (mp10) REVERT: A 698 TYR cc_start: 0.7104 (t80) cc_final: 0.6718 (t80) outliers start: 37 outliers final: 21 residues processed: 243 average time/residue: 0.9387 time to fit residues: 252.5299 Evaluate side-chains 240 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 212 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 637 GLN Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 993 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 2.9990 chunk 110 optimal weight: 0.3980 chunk 24 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 122 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 56 optimal weight: 0.0050 chunk 10 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 64 optimal weight: 0.1980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 HIS ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 HIS ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 917 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1042 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10859 Z= 0.204 Angle : 0.707 11.736 14651 Z= 0.346 Chirality : 0.044 0.287 1581 Planarity : 0.005 0.067 1883 Dihedral : 5.092 56.766 1437 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.56 % Allowed : 25.57 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.23), residues: 1281 helix: 0.27 (0.21), residues: 595 sheet: -1.39 (0.44), residues: 128 loop : -1.39 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 333 HIS 0.015 0.001 HIS A 59 PHE 0.043 0.002 PHE A 667 TYR 0.040 0.001 TYR A 432 ARG 0.013 0.000 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 227 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 326 MET cc_start: 0.4775 (OUTLIER) cc_final: 0.4519 (ptt) REVERT: B 403 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7604 (tp30) REVERT: B 413 LEU cc_start: 0.6429 (OUTLIER) cc_final: 0.6132 (mt) REVERT: B 420 LEU cc_start: 0.6460 (OUTLIER) cc_final: 0.6183 (mm) REVERT: B 422 VAL cc_start: 0.6003 (OUTLIER) cc_final: 0.5733 (t) REVERT: B 537 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7606 (pm20) REVERT: A 164 MET cc_start: 0.7964 (mpp) cc_final: 0.7125 (mpt) REVERT: A 330 ILE cc_start: 0.5708 (mt) cc_final: 0.5484 (mt) REVERT: A 391 ILE cc_start: 0.7599 (OUTLIER) cc_final: 0.7248 (tp) REVERT: A 698 TYR cc_start: 0.7077 (t80) cc_final: 0.6667 (t80) REVERT: A 812 LEU cc_start: 0.7748 (tp) cc_final: 0.7358 (tp) REVERT: A 1039 PHE cc_start: 0.6535 (OUTLIER) cc_final: 0.6174 (m-80) outliers start: 36 outliers final: 19 residues processed: 248 average time/residue: 0.9594 time to fit residues: 261.4763 Evaluate side-chains 238 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 212 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 1039 PHE Chi-restraints excluded: chain A residue 1042 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 74 optimal weight: 0.0980 chunk 56 optimal weight: 7.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 HIS ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 HIS ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 917 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 981 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 10859 Z= 0.331 Angle : 0.781 11.888 14651 Z= 0.390 Chirality : 0.048 0.286 1581 Planarity : 0.005 0.066 1883 Dihedral : 5.313 56.513 1437 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 22.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.98 % Allowed : 25.99 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.23), residues: 1281 helix: 0.13 (0.21), residues: 597 sheet: -1.68 (0.42), residues: 132 loop : -1.45 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 333 HIS 0.009 0.001 HIS A 940 PHE 0.038 0.003 PHE A 667 TYR 0.034 0.002 TYR A 432 ARG 0.014 0.001 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 228 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 403 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7706 (tp30) REVERT: B 413 LEU cc_start: 0.6307 (OUTLIER) cc_final: 0.5971 (mt) REVERT: B 420 LEU cc_start: 0.6352 (OUTLIER) cc_final: 0.5977 (mm) REVERT: B 422 VAL cc_start: 0.5712 (OUTLIER) cc_final: 0.5454 (t) REVERT: B 537 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7563 (pm20) REVERT: A 330 ILE cc_start: 0.5951 (mt) cc_final: 0.5697 (mt) REVERT: A 391 ILE cc_start: 0.7702 (OUTLIER) cc_final: 0.7362 (tp) REVERT: A 441 MET cc_start: 0.6863 (ppp) cc_final: 0.6539 (ppp) REVERT: A 698 TYR cc_start: 0.7287 (t80) cc_final: 0.6877 (t80) outliers start: 41 outliers final: 23 residues processed: 248 average time/residue: 0.8733 time to fit residues: 240.3834 Evaluate side-chains 253 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 225 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 417 ASN Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 957 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 75 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 HIS A 202 ASN ** A 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 HIS ** A 917 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1042 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10859 Z= 0.242 Angle : 0.743 11.665 14651 Z= 0.368 Chirality : 0.045 0.291 1581 Planarity : 0.005 0.068 1883 Dihedral : 5.285 58.595 1437 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 20.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 3.39 % Allowed : 26.93 % Favored : 69.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.23), residues: 1281 helix: 0.19 (0.21), residues: 594 sheet: -1.60 (0.43), residues: 127 loop : -1.40 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 333 HIS 0.009 0.001 HIS A 59 PHE 0.042 0.002 PHE A 667 TYR 0.035 0.002 TYR A 432 ARG 0.013 0.000 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 234 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 403 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7720 (tp30) REVERT: B 413 LEU cc_start: 0.6297 (OUTLIER) cc_final: 0.5885 (mp) REVERT: B 422 VAL cc_start: 0.6026 (OUTLIER) cc_final: 0.5720 (t) REVERT: B 537 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7531 (pm20) REVERT: A 109 GLU cc_start: 0.7858 (mp0) cc_final: 0.7602 (mp0) REVERT: A 123 MET cc_start: 0.5629 (pp-130) cc_final: 0.5333 (pp-130) REVERT: A 296 GLN cc_start: 0.7446 (tp40) cc_final: 0.6130 (mt0) REVERT: A 330 ILE cc_start: 0.5897 (mt) cc_final: 0.5621 (mt) REVERT: A 441 MET cc_start: 0.6779 (ppp) cc_final: 0.6508 (ppp) REVERT: A 698 TYR cc_start: 0.7230 (t80) cc_final: 0.6817 (t80) outliers start: 34 outliers final: 20 residues processed: 253 average time/residue: 0.9489 time to fit residues: 264.3959 Evaluate side-chains 246 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 223 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 957 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 0.1980 chunk 117 optimal weight: 8.9990 chunk 106 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 113 optimal weight: 7.9990 overall best weight: 1.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 GLN ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 917 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1042 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 10859 Z= 0.319 Angle : 0.982 59.199 14651 Z= 0.546 Chirality : 0.048 0.576 1581 Planarity : 0.006 0.138 1883 Dihedral : 5.263 58.611 1437 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 23.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.33 % Favored : 93.59 % Rotamer: Outliers : 2.79 % Allowed : 27.94 % Favored : 69.26 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.23), residues: 1281 helix: 0.19 (0.21), residues: 594 sheet: -1.59 (0.44), residues: 127 loop : -1.41 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 333 HIS 0.172 0.004 HIS A 59 PHE 0.041 0.002 PHE A 667 TYR 0.030 0.002 TYR A 432 ARG 0.011 0.000 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 221 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 403 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7715 (tp30) REVERT: B 419 LYS cc_start: 0.7421 (OUTLIER) cc_final: 0.6463 (tmmt) REVERT: B 422 VAL cc_start: 0.6049 (OUTLIER) cc_final: 0.5745 (t) REVERT: B 499 GLN cc_start: 0.7246 (OUTLIER) cc_final: 0.6889 (tm130) REVERT: B 537 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7504 (pm20) REVERT: A 109 GLU cc_start: 0.7851 (mp0) cc_final: 0.7595 (mp0) REVERT: A 123 MET cc_start: 0.5599 (pp-130) cc_final: 0.4950 (pp-130) REVERT: A 296 GLN cc_start: 0.7445 (tp40) cc_final: 0.6130 (mt0) REVERT: A 330 ILE cc_start: 0.5902 (mt) cc_final: 0.5625 (mt) REVERT: A 391 ILE cc_start: 0.7686 (OUTLIER) cc_final: 0.7337 (tp) REVERT: A 441 MET cc_start: 0.6785 (ppp) cc_final: 0.6547 (ppp) REVERT: A 698 TYR cc_start: 0.7236 (t80) cc_final: 0.6822 (t80) outliers start: 27 outliers final: 20 residues processed: 237 average time/residue: 0.8822 time to fit residues: 231.5696 Evaluate side-chains 241 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 216 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 419 LYS Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 499 GLN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 852 ARG Chi-restraints excluded: chain A residue 957 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 74 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 126 optimal weight: 0.0060 chunk 116 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 61 optimal weight: 0.3980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 917 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 10859 Z= 0.319 Angle : 0.982 59.199 14651 Z= 0.546 Chirality : 0.048 0.576 1581 Planarity : 0.006 0.138 1883 Dihedral : 5.263 58.611 1437 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 24.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.33 % Favored : 93.59 % Rotamer: Outliers : 2.62 % Allowed : 28.37 % Favored : 69.01 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.23), residues: 1281 helix: 0.19 (0.21), residues: 594 sheet: -1.59 (0.44), residues: 127 loop : -1.41 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 333 HIS 0.172 0.004 HIS A 59 PHE 0.041 0.002 PHE A 667 TYR 0.030 0.002 TYR A 432 ARG 0.011 0.000 ARG A 141 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 216 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 403 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7715 (tp30) REVERT: B 419 LYS cc_start: 0.7425 (OUTLIER) cc_final: 0.6464 (tmmt) REVERT: B 422 VAL cc_start: 0.6055 (OUTLIER) cc_final: 0.5745 (t) REVERT: B 499 GLN cc_start: 0.7246 (OUTLIER) cc_final: 0.6889 (tm130) REVERT: B 537 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7504 (pm20) REVERT: A 109 GLU cc_start: 0.7851 (mp0) cc_final: 0.7595 (mp0) REVERT: A 123 MET cc_start: 0.5597 (pp-130) cc_final: 0.4950 (pp-130) REVERT: A 296 GLN cc_start: 0.7445 (tp40) cc_final: 0.6130 (mt0) REVERT: A 330 ILE cc_start: 0.5901 (mt) cc_final: 0.5625 (mt) REVERT: A 391 ILE cc_start: 0.7685 (OUTLIER) cc_final: 0.7337 (tp) REVERT: A 441 MET cc_start: 0.6785 (ppp) cc_final: 0.6547 (ppp) REVERT: A 698 TYR cc_start: 0.7236 (t80) cc_final: 0.6822 (t80) outliers start: 25 outliers final: 20 residues processed: 232 average time/residue: 0.8965 time to fit residues: 229.8708 Evaluate side-chains 244 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 219 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 419 LYS Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 499 GLN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 852 ARG Chi-restraints excluded: chain A residue 957 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 0.8980 chunk 107 optimal weight: 0.0370 chunk 30 optimal weight: 7.9990 chunk 92 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 100 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 917 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.216795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.178936 restraints weight = 37002.212| |-----------------------------------------------------------------------------| r_work (start): 0.4347 rms_B_bonded: 4.73 r_work: 0.4137 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4156 r_free = 0.4156 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4154 r_free = 0.4154 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 10859 Z= 0.319 Angle : 0.982 59.199 14651 Z= 0.546 Chirality : 0.048 0.576 1581 Planarity : 0.006 0.138 1883 Dihedral : 5.263 58.611 1437 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 24.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.33 % Favored : 93.59 % Rotamer: Outliers : 2.62 % Allowed : 28.37 % Favored : 69.01 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.23), residues: 1281 helix: 0.19 (0.21), residues: 594 sheet: -1.59 (0.44), residues: 127 loop : -1.41 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 333 HIS 0.172 0.004 HIS A 59 PHE 0.041 0.002 PHE A 667 TYR 0.030 0.002 TYR A 432 ARG 0.011 0.000 ARG A 141 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4599.82 seconds wall clock time: 82 minutes 42.02 seconds (4962.02 seconds total)