Starting phenix.real_space_refine on Thu Feb 15 18:06:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n3n_24141/02_2024/7n3n_24141_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n3n_24141/02_2024/7n3n_24141.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n3n_24141/02_2024/7n3n_24141.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n3n_24141/02_2024/7n3n_24141.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n3n_24141/02_2024/7n3n_24141_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n3n_24141/02_2024/7n3n_24141_updated.pdb" } resolution = 3.33 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= 0.070 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 82 5.16 5 Cl 2 4.86 5 C 8495 2.51 5 N 2140 2.21 5 O 2307 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 458": "OE1" <-> "OE2" Residue "A GLU 475": "OE1" <-> "OE2" Residue "A PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 811": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1106": "OE1" <-> "OE2" Residue "A GLU 1119": "OE1" <-> "OE2" Residue "B GLU 389": "OE1" <-> "OE2" Residue "B PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 483": "OE1" <-> "OE2" Residue "B GLU 834": "OE1" <-> "OE2" Residue "B GLU 865": "OE1" <-> "OE2" Residue "B GLU 1099": "OE1" <-> "OE2" Residue "B GLU 1105": "OE1" <-> "OE2" Residue "B GLU 1106": "OE1" <-> "OE2" Residue "B GLU 1140": "OE1" <-> "OE2" 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: 13026 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 832, 6487 Classifications: {'peptide': 832} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 29, 'TRANS': 802} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 6497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 831, 6497 Classifications: {'peptide': 831} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 29, 'TRANS': 801} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'FUN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'FUN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.64, per 1000 atoms: 0.51 Number of scatterers: 13026 At special positions: 0 Unit cell: (81.32, 155.15, 115.56, 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) Cl 2 17.00 S 82 16.00 O 2307 8.00 N 2140 7.00 C 8495 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 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 Simple disulfide: pdb=" SG CYS B 563 " - pdb=" SG CYS B 568 " 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: 5.62 Conformation dependent library (CDL) restraints added in 2.3 seconds 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3080 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 63 helices and 2 sheets defined 56.0% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.91 Creating SS restraints... Processing helix chain 'A' and resid 288 through 299 Processing helix chain 'A' and resid 308 through 314 Processing helix chain 'A' and resid 317 through 343 Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 362 through 398 removed outlier: 4.354A pdb=" N GLY A 366 " --> pdb=" O PRO A 362 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA A 367 " --> pdb=" O GLU A 363 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A 368 " --> pdb=" O PHE A 364 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N HIS A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 424 Processing helix chain 'A' and resid 429 through 452 removed outlier: 4.405A pdb=" N ILE A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL A 440 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE A 441 " --> pdb=" O VAL A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 475 removed outlier: 3.515A pdb=" N ASN A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 498 Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 501 through 505 removed outlier: 3.622A pdb=" N GLY A 504 " --> pdb=" O ILE A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 541 Processing helix chain 'A' and resid 592 through 596 Processing helix chain 'A' and resid 600 through 632 Proline residue: A 623 - end of helix Processing helix chain 'A' and resid 636 through 641 removed outlier: 5.454A pdb=" N MET A 640 " --> pdb=" O ALA A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 666 Processing helix chain 'A' and resid 674 through 699 removed outlier: 3.502A pdb=" N ILE A 678 " --> pdb=" O ILE A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 729 Processing helix chain 'A' and resid 732 through 751 removed outlier: 3.542A pdb=" N TYR A 751 " --> pdb=" O ILE A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 779 Processing helix chain 'A' and resid 802 through 812 removed outlier: 3.790A pdb=" N PHE A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 848 Processing helix chain 'A' and resid 863 through 873 Processing helix chain 'A' and resid 897 through 912 Processing helix chain 'A' and resid 1035 through 1046 Proline residue: A1040 - end of helix removed outlier: 3.609A pdb=" N THR A1045 " --> pdb=" O TYR A1041 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LYS A1046 " --> pdb=" O LEU A1042 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1079 Processing helix chain 'A' and resid 1098 through 1111 Proline residue: A1110 - end of helix Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1136 through 1141 Processing helix chain 'A' and resid 1143 through 1159 Processing helix chain 'A' and resid 1180 through 1190 Processing helix chain 'B' and resid 288 through 299 removed outlier: 3.941A pdb=" N VAL B 293 " --> pdb=" O LYS B 289 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ARG B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 306 through 314 removed outlier: 4.314A pdb=" N TRP B 310 " --> pdb=" O ILE B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 343 Processing helix chain 'B' and resid 352 through 359 Processing helix chain 'B' and resid 362 through 397 removed outlier: 3.806A pdb=" N ALA B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 424 removed outlier: 3.626A pdb=" N ARG B 410 " --> pdb=" O ILE B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 453 removed outlier: 3.671A pdb=" N ALA B 434 " --> pdb=" O TRP B 430 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLN B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL B 437 " --> pdb=" O LYS B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 462 Proline residue: B 462 - end of helix No H-bonds generated for 'chain 'B' and resid 458 through 462' Processing helix chain 'B' and resid 470 through 477 removed outlier: 4.193A pdb=" N GLU B 475 " --> pdb=" O GLU B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 494 Processing helix chain 'B' and resid 501 through 505 removed outlier: 4.405A pdb=" N ALA B 505 " --> pdb=" O ILE B 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 501 through 505' Processing helix chain 'B' and resid 517 through 542 removed outlier: 3.750A pdb=" N LEU B 524 " --> pdb=" O LYS B 520 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA B 525 " --> pdb=" O GLY B 521 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU B 531 " --> pdb=" O LEU B 527 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N VAL B 532 " --> pdb=" O ILE B 528 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY B 541 " --> pdb=" O ALA B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 568 No H-bonds generated for 'chain 'B' and resid 566 through 568' Processing helix chain 'B' and resid 592 through 596 Processing helix chain 'B' and resid 600 through 631 Proline residue: B 623 - end of helix Processing helix chain 'B' and resid 637 through 641 removed outlier: 4.474A pdb=" N MET B 640 " --> pdb=" O ALA B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 666 removed outlier: 3.928A pdb=" N LEU B 663 " --> pdb=" O PHE B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 698 Proline residue: B 676 - end of helix Processing helix chain 'B' and resid 713 through 730 removed outlier: 3.658A pdb=" N ILE B 730 " --> pdb=" O VAL B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 750 Processing helix chain 'B' and resid 763 through 778 removed outlier: 4.164A pdb=" N ASN B 769 " --> pdb=" O LEU B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 811 removed outlier: 3.858A pdb=" N PHE B 811 " --> pdb=" O LEU B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 848 Processing helix chain 'B' and resid 863 through 873 Processing helix chain 'B' and resid 897 through 912 removed outlier: 3.849A pdb=" N PHE B 907 " --> pdb=" O TYR B 903 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS B 908 " --> pdb=" O ILE B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 1035 through 1044 Proline residue: B1040 - end of helix Processing helix chain 'B' and resid 1065 through 1079 removed outlier: 3.536A pdb=" N PHE B1079 " --> pdb=" O LEU B1075 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1111 Proline residue: B1110 - end of helix Processing helix chain 'B' and resid 1120 through 1129 Processing helix chain 'B' and resid 1136 through 1141 Processing helix chain 'B' and resid 1143 through 1159 Processing helix chain 'B' and resid 1180 through 1190 Processing sheet with id= A, first strand: chain 'A' and resid 1085 through 1088 removed outlier: 3.895A pdb=" N ASP A1085 " --> pdb=" O ILE A1054 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG A1055 " --> pdb=" O ILE A1024 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ILE A1165 " --> pdb=" O ASP A1025 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N TRP A1027 " --> pdb=" O ILE A1165 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL A1167 " --> pdb=" O TRP A1027 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A1197 " --> pdb=" O ARG A 921 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 1085 through 1089 removed outlier: 3.561A pdb=" N ARG B1055 " --> pdb=" O ILE B1024 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLY B1059 " --> pdb=" O TRP B1028 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE B1165 " --> pdb=" O ASP B1025 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N TRP B1027 " --> pdb=" O ILE B1165 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL B1167 " --> pdb=" O TRP B1027 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N GLY B 887 " --> pdb=" O MET B 794 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU B 817 " --> pdb=" O CYS B 791 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N VAL B 793 " --> pdb=" O LEU B 817 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE B 819 " --> pdb=" O VAL B 793 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA B 856 " --> pdb=" O HIS B 822 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N HIS B 824 " --> pdb=" O ALA B 856 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL B 858 " --> pdb=" O HIS B 824 " (cutoff:3.500A) 673 hydrogen bonds defined for protein. 2004 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: 3.85 Time building geometry restraints manager: 5.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2136 1.32 - 1.45: 3490 1.45 - 1.57: 7550 1.57 - 1.69: 0 1.69 - 1.82: 142 Bond restraints: 13318 Sorted by residual: bond pdb=" C4 FUN A1301 " pdb=" N2 FUN A1301 " ideal model delta sigma weight residual 1.340 1.451 -0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" C4 FUN B1301 " pdb=" N2 FUN B1301 " ideal model delta sigma weight residual 1.340 1.450 -0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" CA ASN A 814 " pdb=" C ASN A 814 " ideal model delta sigma weight residual 1.526 1.463 0.062 1.31e-02 5.83e+03 2.26e+01 bond pdb=" CA LYS A 813 " pdb=" C LYS A 813 " ideal model delta sigma weight residual 1.524 1.477 0.046 1.27e-02 6.20e+03 1.33e+01 bond pdb=" C7 FUN B1301 " pdb=" C8 FUN B1301 " ideal model delta sigma weight residual 1.429 1.360 0.069 2.00e-02 2.50e+03 1.19e+01 ... (remaining 13313 not shown) Histogram of bond angle deviations from ideal: 98.91 - 105.96: 263 105.96 - 113.00: 7282 113.00 - 120.05: 4633 120.05 - 127.09: 5739 127.09 - 134.14: 148 Bond angle restraints: 18065 Sorted by residual: angle pdb=" N ARG A 482 " pdb=" CA ARG A 482 " pdb=" C ARG A 482 " ideal model delta sigma weight residual 111.28 121.00 -9.72 1.09e+00 8.42e-01 7.95e+01 angle pdb=" N PHE A 481 " pdb=" CA PHE A 481 " pdb=" C PHE A 481 " ideal model delta sigma weight residual 110.80 123.72 -12.92 2.13e+00 2.20e-01 3.68e+01 angle pdb=" O1 FUN B1301 " pdb=" S1 FUN B1301 " pdb=" O2 FUN B1301 " ideal model delta sigma weight residual 119.17 101.12 18.05 3.00e+00 1.11e-01 3.62e+01 angle pdb=" O1 FUN A1301 " pdb=" S1 FUN A1301 " pdb=" O2 FUN A1301 " ideal model delta sigma weight residual 119.17 101.37 17.80 3.00e+00 1.11e-01 3.52e+01 angle pdb=" N PRO A 479 " pdb=" CA PRO A 479 " pdb=" C PRO A 479 " ideal model delta sigma weight residual 113.53 119.48 -5.95 1.39e+00 5.18e-01 1.83e+01 ... (remaining 18060 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 7143 17.71 - 35.41: 591 35.41 - 53.12: 99 53.12 - 70.83: 24 70.83 - 88.53: 7 Dihedral angle restraints: 7864 sinusoidal: 3071 harmonic: 4793 Sorted by residual: dihedral pdb=" C PHE A 481 " pdb=" N PHE A 481 " pdb=" CA PHE A 481 " pdb=" CB PHE A 481 " ideal model delta harmonic sigma weight residual -122.60 -142.17 19.57 0 2.50e+00 1.60e-01 6.13e+01 dihedral pdb=" N PHE A 481 " pdb=" C PHE A 481 " pdb=" CA PHE A 481 " pdb=" CB PHE A 481 " ideal model delta harmonic sigma weight residual 122.80 142.01 -19.21 0 2.50e+00 1.60e-01 5.90e+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 -86.00 -146.43 60.43 1 1.00e+01 1.00e-02 4.86e+01 ... (remaining 7861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.187: 2070 0.187 - 0.373: 9 0.373 - 0.560: 2 0.560 - 0.747: 0 0.747 - 0.933: 1 Chirality restraints: 2082 Sorted by residual: chirality pdb=" CA PHE A 481 " pdb=" N PHE A 481 " pdb=" C PHE A 481 " pdb=" CB PHE A 481 " both_signs ideal model delta sigma weight residual False 2.51 1.58 0.93 2.00e-01 2.50e+01 2.18e+01 chirality pdb=" CA PHE A 811 " pdb=" N PHE A 811 " pdb=" C PHE A 811 " pdb=" CB PHE A 811 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.80e+00 chirality pdb=" CA ARG A 482 " pdb=" N ARG A 482 " pdb=" C ARG A 482 " pdb=" CB ARG A 482 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.42e+00 ... (remaining 2079 not shown) Planarity restraints: 2243 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 300 " -0.023 2.00e-02 2.50e+03 2.57e-02 1.65e+01 pdb=" CG TRP A 300 " 0.067 2.00e-02 2.50e+03 pdb=" CD1 TRP A 300 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TRP A 300 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 300 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP A 300 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 300 " -0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 300 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 300 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 300 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 728 " -0.024 2.00e-02 2.50e+03 2.16e-02 8.14e+00 pdb=" CG PHE B 728 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE B 728 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE B 728 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 728 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 728 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE B 728 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 728 " -0.028 2.00e-02 2.50e+03 2.05e-02 7.35e+00 pdb=" CG PHE A 728 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE A 728 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 728 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 728 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 728 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 728 " -0.016 2.00e-02 2.50e+03 ... (remaining 2240 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 22 2.39 - 3.01: 7368 3.01 - 3.64: 20459 3.64 - 4.27: 29448 4.27 - 4.90: 49251 Nonbonded interactions: 106548 Sorted by model distance: nonbonded pdb=" CB PHE A 346 " pdb=" CD2 LEU A 355 " model vdw 1.756 3.860 nonbonded pdb=" O ASN A 757 " pdb=" OG1 THR A 762 " model vdw 2.173 2.440 nonbonded pdb=" O GLN B 763 " pdb=" OG1 THR B 766 " model vdw 2.215 2.440 nonbonded pdb=" O TYR A 746 " pdb=" OG1 THR A 750 " model vdw 2.226 2.440 nonbonded pdb=" O VAL B 450 " pdb=" OG1 THR B 453 " model vdw 2.228 2.440 ... (remaining 106543 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' and (resid 287 through 926 or resid 1020 through 1208 or resid 1301)) \ selection = (chain 'B' and (resid 287 through 345 or (resid 346 through 348 and (name N or n \ ame CA or name C or name O or name CB )) or resid 349 through 1208 or resid 1301 \ )) } 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: 3.550 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: 13.920 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 36.850 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 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 0.111 13318 Z= 0.327 Angle : 0.832 18.053 18065 Z= 0.456 Chirality : 0.054 0.933 2082 Planarity : 0.006 0.063 2243 Dihedral : 13.626 88.533 4775 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.22 % Allowed : 0.57 % Favored : 99.21 % Cbeta Deviations : 0.06 % 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: -0.92 (0.19), residues: 1655 helix: 0.40 (0.16), residues: 940 sheet: -0.87 (0.47), residues: 129 loop : -2.21 (0.21), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP A 300 HIS 0.003 0.001 HIS B 773 PHE 0.049 0.002 PHE B 728 TYR 0.024 0.002 TYR A 353 ARG 0.009 0.001 ARG B 898 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 236 time to evaluate : 1.409 Fit side-chains REVERT: A 402 MET cc_start: 0.6509 (tmm) cc_final: 0.3596 (mmt) REVERT: A 590 PHE cc_start: 0.6053 (m-80) cc_final: 0.5678 (m-80) REVERT: B 748 TYR cc_start: 0.7324 (t80) cc_final: 0.7121 (t80) REVERT: B 1128 GLU cc_start: 0.6178 (pt0) cc_final: 0.5894 (pt0) outliers start: 3 outliers final: 0 residues processed: 237 average time/residue: 0.2179 time to fit residues: 78.1372 Evaluate side-chains 198 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 0.3980 chunk 125 optimal weight: 0.2980 chunk 69 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 84 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 79 optimal weight: 0.4980 chunk 96 optimal weight: 3.9990 chunk 150 optimal weight: 0.0030 overall best weight: 0.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.0925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13318 Z= 0.174 Angle : 0.563 13.444 18065 Z= 0.292 Chirality : 0.042 0.271 2082 Planarity : 0.004 0.059 2243 Dihedral : 6.559 83.108 1780 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.50 % Allowed : 8.39 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.52 (0.20), residues: 1655 helix: 0.82 (0.17), residues: 944 sheet: -0.77 (0.45), residues: 128 loop : -2.22 (0.22), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 300 HIS 0.007 0.001 HIS A1067 PHE 0.041 0.002 PHE B 728 TYR 0.038 0.001 TYR A 739 ARG 0.007 0.000 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 220 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 402 MET cc_start: 0.6731 (tmm) cc_final: 0.3650 (mmt) REVERT: A 590 PHE cc_start: 0.6303 (m-80) cc_final: 0.5892 (m-80) REVERT: B 368 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8461 (mp) outliers start: 7 outliers final: 2 residues processed: 222 average time/residue: 0.2114 time to fit residues: 71.7636 Evaluate side-chains 199 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 196 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 1067 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 102 optimal weight: 0.3980 chunk 41 optimal weight: 9.9990 chunk 151 optimal weight: 0.9980 chunk 163 optimal weight: 0.4980 chunk 134 optimal weight: 0.5980 chunk 149 optimal weight: 0.5980 chunk 51 optimal weight: 0.0770 chunk 121 optimal weight: 3.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 799 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13318 Z= 0.173 Angle : 0.530 8.576 18065 Z= 0.276 Chirality : 0.041 0.155 2082 Planarity : 0.004 0.058 2243 Dihedral : 6.377 82.639 1780 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.58 % Allowed : 11.25 % Favored : 87.17 % Cbeta Deviations : 0.00 % 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: -0.34 (0.20), residues: 1655 helix: 1.01 (0.17), residues: 947 sheet: -0.78 (0.44), residues: 129 loop : -2.21 (0.22), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 300 HIS 0.006 0.001 HIS A1067 PHE 0.039 0.001 PHE B 728 TYR 0.018 0.001 TYR A 353 ARG 0.005 0.000 ARG A1064 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 212 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 MET cc_start: 0.6683 (tmm) cc_final: 0.3653 (mmt) REVERT: A 590 PHE cc_start: 0.6356 (m-80) cc_final: 0.5918 (m-80) REVERT: A 626 PHE cc_start: 0.5419 (OUTLIER) cc_final: 0.4922 (t80) REVERT: B 368 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8480 (mp) outliers start: 22 outliers final: 12 residues processed: 223 average time/residue: 0.2128 time to fit residues: 72.8951 Evaluate side-chains 207 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 193 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 724 CYS Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 453 THR Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 721 ILE Chi-restraints excluded: chain B residue 832 MET Chi-restraints excluded: chain B residue 1067 HIS Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1209 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 149 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 72 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 151 optimal weight: 0.0970 chunk 160 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 814 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13318 Z= 0.226 Angle : 0.557 9.965 18065 Z= 0.287 Chirality : 0.042 0.240 2082 Planarity : 0.004 0.057 2243 Dihedral : 6.296 82.377 1780 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.29 % Allowed : 13.05 % Favored : 84.66 % Cbeta Deviations : 0.00 % 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: -0.27 (0.20), residues: 1655 helix: 1.05 (0.17), residues: 947 sheet: -0.55 (0.44), residues: 120 loop : -2.18 (0.22), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 300 HIS 0.007 0.001 HIS A1067 PHE 0.031 0.002 PHE B 728 TYR 0.031 0.001 TYR A 739 ARG 0.005 0.000 ARG A1112 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 207 time to evaluate : 1.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 MET cc_start: 0.6673 (tmm) cc_final: 0.3650 (mmt) REVERT: A 590 PHE cc_start: 0.6452 (m-80) cc_final: 0.6045 (m-80) REVERT: A 626 PHE cc_start: 0.5449 (OUTLIER) cc_final: 0.4888 (t80) REVERT: A 678 ILE cc_start: 0.7571 (mt) cc_final: 0.7259 (mt) REVERT: A 732 TRP cc_start: 0.6179 (p-90) cc_final: 0.5922 (p-90) REVERT: B 368 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8504 (mp) REVERT: B 1101 ILE cc_start: 0.8120 (mt) cc_final: 0.7897 (mt) outliers start: 32 outliers final: 21 residues processed: 223 average time/residue: 0.2196 time to fit residues: 76.2187 Evaluate side-chains 216 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 193 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 724 CYS Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 453 THR Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 589 ASN Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 721 ILE Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 1067 HIS Chi-restraints excluded: chain B residue 1087 MET Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1209 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 133 optimal weight: 0.9980 chunk 91 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 66 optimal weight: 0.4980 chunk 136 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 81 optimal weight: 0.0570 chunk 144 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 814 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13318 Z= 0.216 Angle : 0.547 7.857 18065 Z= 0.284 Chirality : 0.041 0.191 2082 Planarity : 0.004 0.061 2243 Dihedral : 6.197 81.674 1780 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.44 % Allowed : 14.70 % Favored : 82.87 % Cbeta Deviations : 0.00 % 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: -0.23 (0.20), residues: 1655 helix: 1.08 (0.17), residues: 949 sheet: -0.74 (0.43), residues: 126 loop : -2.15 (0.22), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 300 HIS 0.007 0.001 HIS A1067 PHE 0.031 0.002 PHE B 728 TYR 0.033 0.001 TYR A 739 ARG 0.004 0.000 ARG A 546 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 201 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 402 MET cc_start: 0.6641 (tmm) cc_final: 0.3596 (mmt) REVERT: A 590 PHE cc_start: 0.6426 (m-80) cc_final: 0.6115 (m-80) REVERT: A 626 PHE cc_start: 0.5466 (OUTLIER) cc_final: 0.5008 (t80) REVERT: A 732 TRP cc_start: 0.6176 (p-90) cc_final: 0.5916 (p-90) REVERT: B 368 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8501 (mp) outliers start: 34 outliers final: 23 residues processed: 221 average time/residue: 0.2108 time to fit residues: 72.3667 Evaluate side-chains 217 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 192 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 724 CYS Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1092 ILE Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 453 THR Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 589 ASN Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 721 ILE Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 832 MET Chi-restraints excluded: chain B residue 1067 HIS Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1209 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 53 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 160 optimal weight: 0.6980 chunk 133 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 154 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13318 Z= 0.224 Angle : 0.564 7.879 18065 Z= 0.293 Chirality : 0.042 0.188 2082 Planarity : 0.004 0.060 2243 Dihedral : 6.150 80.886 1780 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.08 % Allowed : 16.13 % Favored : 81.79 % Cbeta Deviations : 0.00 % 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: -0.25 (0.20), residues: 1655 helix: 1.08 (0.17), residues: 948 sheet: -0.80 (0.43), residues: 128 loop : -2.17 (0.22), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 300 HIS 0.007 0.001 HIS A1067 PHE 0.033 0.002 PHE B 659 TYR 0.034 0.001 TYR A 739 ARG 0.006 0.000 ARG B 898 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 191 time to evaluate : 1.446 Fit side-chains revert: symmetry clash REVERT: A 303 MET cc_start: 0.3972 (ttm) cc_final: 0.3733 (ttm) REVERT: A 402 MET cc_start: 0.6637 (tmm) cc_final: 0.3623 (mmt) REVERT: A 590 PHE cc_start: 0.6494 (m-80) cc_final: 0.6169 (m-80) REVERT: A 626 PHE cc_start: 0.5491 (OUTLIER) cc_final: 0.5031 (t80) REVERT: A 732 TRP cc_start: 0.6182 (p-90) cc_final: 0.5931 (p-90) REVERT: B 368 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8523 (mp) outliers start: 29 outliers final: 26 residues processed: 206 average time/residue: 0.2088 time to fit residues: 67.3897 Evaluate side-chains 212 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 184 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1092 ILE Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 453 THR Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 589 ASN Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 721 ILE Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 832 MET Chi-restraints excluded: chain B residue 1067 HIS Chi-restraints excluded: chain B residue 1087 MET Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1162 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 18 optimal weight: 0.1980 chunk 91 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 135 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 159 optimal weight: 0.9990 chunk 100 optimal weight: 0.2980 chunk 97 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13318 Z= 0.209 Angle : 0.561 8.638 18065 Z= 0.292 Chirality : 0.042 0.195 2082 Planarity : 0.004 0.059 2243 Dihedral : 6.079 80.035 1780 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.29 % Allowed : 17.13 % Favored : 80.57 % Cbeta Deviations : 0.00 % 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: -0.23 (0.20), residues: 1655 helix: 1.09 (0.17), residues: 949 sheet: -0.79 (0.43), residues: 128 loop : -2.15 (0.22), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A 300 HIS 0.008 0.001 HIS A1067 PHE 0.033 0.002 PHE B 728 TYR 0.034 0.001 TYR A 739 ARG 0.006 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 192 time to evaluate : 1.393 Fit side-chains revert: symmetry clash REVERT: A 402 MET cc_start: 0.6633 (tmm) cc_final: 0.3625 (mmt) REVERT: A 590 PHE cc_start: 0.6533 (m-80) cc_final: 0.6208 (m-80) REVERT: A 626 PHE cc_start: 0.5463 (OUTLIER) cc_final: 0.5026 (t80) REVERT: A 677 ILE cc_start: 0.5810 (mt) cc_final: 0.5519 (mt) REVERT: A 732 TRP cc_start: 0.6176 (p-90) cc_final: 0.5937 (p-90) REVERT: B 297 LEU cc_start: 0.8413 (mt) cc_final: 0.8158 (pp) REVERT: B 368 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8514 (mp) outliers start: 32 outliers final: 23 residues processed: 210 average time/residue: 0.1994 time to fit residues: 65.5464 Evaluate side-chains 212 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 187 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1092 ILE Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 453 THR Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 589 ASN Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 721 ILE Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 1067 HIS Chi-restraints excluded: chain B residue 1087 MET Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1162 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 63 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 79 optimal weight: 0.0010 chunk 14 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 145 optimal weight: 0.9980 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13318 Z= 0.232 Angle : 0.580 10.250 18065 Z= 0.299 Chirality : 0.042 0.202 2082 Planarity : 0.004 0.057 2243 Dihedral : 6.044 79.345 1780 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.29 % Allowed : 17.49 % Favored : 80.22 % Cbeta Deviations : 0.00 % 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: -0.28 (0.20), residues: 1655 helix: 1.05 (0.17), residues: 955 sheet: -0.82 (0.44), residues: 128 loop : -2.20 (0.22), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP A 300 HIS 0.007 0.001 HIS A1067 PHE 0.038 0.002 PHE B 728 TYR 0.033 0.001 TYR A 739 ARG 0.007 0.000 ARG B 898 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 192 time to evaluate : 1.512 Fit side-chains revert: symmetry clash REVERT: A 402 MET cc_start: 0.6655 (tmm) cc_final: 0.3633 (mmt) REVERT: A 590 PHE cc_start: 0.6605 (m-80) cc_final: 0.6261 (m-80) REVERT: A 626 PHE cc_start: 0.5491 (OUTLIER) cc_final: 0.5040 (t80) REVERT: A 677 ILE cc_start: 0.5745 (mt) cc_final: 0.5360 (mt) REVERT: A 732 TRP cc_start: 0.6207 (p-90) cc_final: 0.5963 (p-90) REVERT: B 297 LEU cc_start: 0.8441 (mt) cc_final: 0.8178 (pp) REVERT: B 368 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8526 (mp) REVERT: B 495 PHE cc_start: 0.7523 (t80) cc_final: 0.7305 (t80) REVERT: B 659 PHE cc_start: 0.6891 (t80) cc_final: 0.6105 (t80) REVERT: B 1072 MET cc_start: 0.7711 (tpt) cc_final: 0.7497 (tpt) outliers start: 32 outliers final: 28 residues processed: 209 average time/residue: 0.2088 time to fit residues: 67.9057 Evaluate side-chains 215 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 185 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1092 ILE Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 453 THR Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 589 ASN Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 721 ILE Chi-restraints excluded: chain B residue 724 CYS Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 832 MET Chi-restraints excluded: chain B residue 1067 HIS Chi-restraints excluded: chain B residue 1087 MET Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1172 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 153 optimal weight: 0.0770 chunk 139 optimal weight: 0.0670 chunk 149 optimal weight: 0.0020 chunk 89 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 chunk 117 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 141 optimal weight: 0.7980 chunk 148 optimal weight: 0.6980 chunk 97 optimal weight: 8.9990 overall best weight: 0.3284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1067 HIS B 506 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13318 Z= 0.177 Angle : 0.563 16.039 18065 Z= 0.287 Chirality : 0.041 0.218 2082 Planarity : 0.004 0.058 2243 Dihedral : 5.894 77.571 1780 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.08 % Allowed : 17.99 % Favored : 79.93 % Cbeta Deviations : 0.00 % 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: -0.19 (0.20), residues: 1655 helix: 1.12 (0.17), residues: 957 sheet: -0.80 (0.43), residues: 129 loop : -2.18 (0.22), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP A 300 HIS 0.008 0.001 HIS A1067 PHE 0.037 0.001 PHE B 728 TYR 0.033 0.001 TYR A 739 ARG 0.008 0.000 ARG B 898 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 186 time to evaluate : 1.446 Fit side-chains revert: symmetry clash REVERT: A 402 MET cc_start: 0.6617 (tmm) cc_final: 0.3638 (mmt) REVERT: A 590 PHE cc_start: 0.6662 (m-80) cc_final: 0.6324 (m-80) REVERT: A 626 PHE cc_start: 0.5367 (OUTLIER) cc_final: 0.4980 (t80) REVERT: A 732 TRP cc_start: 0.6186 (p-90) cc_final: 0.5927 (p-90) REVERT: B 297 LEU cc_start: 0.8436 (mt) cc_final: 0.8172 (pp) REVERT: B 368 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8483 (mp) outliers start: 29 outliers final: 23 residues processed: 203 average time/residue: 0.2057 time to fit residues: 65.0526 Evaluate side-chains 208 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 183 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 724 CYS Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 589 ASN Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 721 ILE Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 832 MET Chi-restraints excluded: chain B residue 1067 HIS Chi-restraints excluded: chain B residue 1087 MET Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1162 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 157 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 109 optimal weight: 0.4980 chunk 165 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 101 optimal weight: 0.0970 chunk 80 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 ASN B 786 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13318 Z= 0.213 Angle : 0.601 15.636 18065 Z= 0.302 Chirality : 0.042 0.226 2082 Planarity : 0.004 0.060 2243 Dihedral : 5.870 77.016 1780 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.01 % Allowed : 18.21 % Favored : 79.78 % Cbeta Deviations : 0.00 % 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: -0.23 (0.20), residues: 1655 helix: 1.09 (0.17), residues: 954 sheet: -0.85 (0.43), residues: 129 loop : -2.17 (0.22), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 300 HIS 0.008 0.001 HIS A1067 PHE 0.032 0.001 PHE B 728 TYR 0.033 0.001 TYR A 739 ARG 0.008 0.000 ARG B 898 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 194 time to evaluate : 1.549 Fit side-chains revert: symmetry clash REVERT: A 364 PHE cc_start: 0.6582 (m-10) cc_final: 0.6364 (m-80) REVERT: A 402 MET cc_start: 0.6636 (tmm) cc_final: 0.3633 (mmt) REVERT: A 590 PHE cc_start: 0.6725 (m-80) cc_final: 0.6387 (m-80) REVERT: A 626 PHE cc_start: 0.5374 (OUTLIER) cc_final: 0.4986 (t80) REVERT: A 732 TRP cc_start: 0.6227 (p-90) cc_final: 0.5976 (p-90) REVERT: B 297 LEU cc_start: 0.8437 (mt) cc_final: 0.8203 (pp) REVERT: B 368 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8475 (mp) REVERT: B 898 ARG cc_start: 0.6791 (ttp-110) cc_final: 0.6570 (ttm110) outliers start: 28 outliers final: 24 residues processed: 208 average time/residue: 0.2060 time to fit residues: 67.2492 Evaluate side-chains 213 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 187 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 589 ASN Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 721 ILE Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 832 MET Chi-restraints excluded: chain B residue 1067 HIS Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1172 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 135 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 ASN B 786 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.218425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.164843 restraints weight = 16509.003| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 2.44 r_work: 0.3818 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 13318 Z= 0.250 Angle : 0.617 15.709 18065 Z= 0.312 Chirality : 0.043 0.224 2082 Planarity : 0.004 0.067 2243 Dihedral : 5.881 77.082 1780 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.86 % Allowed : 18.21 % Favored : 79.93 % Cbeta Deviations : 0.00 % 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: -0.25 (0.20), residues: 1655 helix: 1.07 (0.17), residues: 953 sheet: -0.93 (0.43), residues: 129 loop : -2.15 (0.23), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 300 HIS 0.008 0.001 HIS A1067 PHE 0.038 0.002 PHE B 659 TYR 0.034 0.001 TYR A 739 ARG 0.007 0.000 ARG B 898 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2951.89 seconds wall clock time: 54 minutes 20.51 seconds (3260.51 seconds total)