Starting phenix.real_space_refine on Mon Mar 11 00:03:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxu_40859/03_2024/8sxu_40859.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxu_40859/03_2024/8sxu_40859.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxu_40859/03_2024/8sxu_40859.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxu_40859/03_2024/8sxu_40859.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxu_40859/03_2024/8sxu_40859.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxu_40859/03_2024/8sxu_40859.pdb" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.029 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 P 10 5.49 5 S 20 5.16 5 C 3981 2.51 5 N 1064 2.21 5 O 1132 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 430": "OD1" <-> "OD2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "A PHE 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 539": "OD1" <-> "OD2" Residue "A TYR 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 673": "OE1" <-> "OE2" Residue "A GLU 709": "OE1" <-> "OE2" Residue "A GLU 841": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6207 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5987 Classifications: {'peptide': 726} Link IDs: {'PTRANS': 33, 'TRANS': 692} Chain breaks: 1 Chain: "C" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 220 Classifications: {'RNA': 10} Modifications used: {'rna2p_pur': 5, 'rna3p_pur': 5} Link IDs: {'rna2p': 4, 'rna3p': 5} Time building chain proxies: 3.93, per 1000 atoms: 0.63 Number of scatterers: 6207 At special positions: 0 Unit cell: (82.6, 82.6, 101.598, 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 20 16.00 P 10 15.00 O 1132 8.00 N 1064 7.00 C 3981 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: 2.44 Conformation dependent library (CDL) restraints added in 1.2 seconds 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1396 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 4 sheets defined 58.8% alpha, 6.3% beta 0 base pairs and 1 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'A' and resid 255 through 258 Processing helix chain 'A' and resid 259 through 275 removed outlier: 4.127A pdb=" N PHE A 274 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 310 removed outlier: 3.937A pdb=" N LEU A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 421 removed outlier: 3.770A pdb=" N GLN A 408 " --> pdb=" O PRO A 404 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR A 409 " --> pdb=" O THR A 405 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU A 413 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN A 421 " --> pdb=" O HIS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 436 removed outlier: 3.796A pdb=" N THR A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE A 432 " --> pdb=" O GLU A 428 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 433 " --> pdb=" O MET A 429 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR A 436 " --> pdb=" O PHE A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 450 Processing helix chain 'A' and resid 454 through 464 removed outlier: 4.069A pdb=" N ILE A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL A 459 " --> pdb=" O GLY A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 484 removed outlier: 3.866A pdb=" N GLN A 482 " --> pdb=" O ALA A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 503 removed outlier: 3.727A pdb=" N LEU A 488 " --> pdb=" O TYR A 484 " (cutoff:3.500A) Proline residue: A 490 - end of helix removed outlier: 4.230A pdb=" N LEU A 493 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE A 499 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A 501 " --> pdb=" O GLN A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 510 Processing helix chain 'A' and resid 526 through 528 No H-bonds generated for 'chain 'A' and resid 526 through 528' Processing helix chain 'A' and resid 537 through 553 removed outlier: 3.542A pdb=" N LYS A 545 " --> pdb=" O LYS A 541 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A 546 " --> pdb=" O ILE A 542 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 547 " --> pdb=" O LEU A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 559 Processing helix chain 'A' and resid 572 through 589 removed outlier: 4.321A pdb=" N ILE A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL A 582 " --> pdb=" O LYS A 578 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE A 583 " --> pdb=" O SER A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 620 Processing helix chain 'A' and resid 624 through 634 Processing helix chain 'A' and resid 662 through 682 removed outlier: 4.550A pdb=" N LEU A 666 " --> pdb=" O PRO A 662 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 670 " --> pdb=" O LEU A 666 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 675 " --> pdb=" O VAL A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 730 removed outlier: 3.740A pdb=" N LEU A 721 " --> pdb=" O ASN A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.875A pdb=" N GLN A 752 " --> pdb=" O GLN A 748 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE A 753 " --> pdb=" O THR A 749 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET A 754 " --> pdb=" O GLU A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 778 No H-bonds generated for 'chain 'A' and resid 776 through 778' Processing helix chain 'A' and resid 779 through 796 Proline residue: A 787 - end of helix removed outlier: 3.675A pdb=" N ILE A 792 " --> pdb=" O LEU A 788 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A 794 " --> pdb=" O LYS A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 816 removed outlier: 3.966A pdb=" N ILE A 810 " --> pdb=" O TRP A 806 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASN A 811 " --> pdb=" O VAL A 807 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE A 812 " --> pdb=" O GLY A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 828 removed outlier: 4.204A pdb=" N LYS A 820 " --> pdb=" O ALA A 816 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 822 " --> pdb=" O LEU A 818 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TYR A 823 " --> pdb=" O PRO A 819 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG A 824 " --> pdb=" O LYS A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 849 removed outlier: 3.885A pdb=" N PHE A 837 " --> pdb=" O PRO A 833 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU A 839 " --> pdb=" O THR A 835 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 840 " --> pdb=" O PHE A 836 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TRP A 849 " --> pdb=" O LEU A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 862 Processing helix chain 'A' and resid 874 through 886 removed outlier: 3.778A pdb=" N THR A 886 " --> pdb=" O THR A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 893 removed outlier: 4.156A pdb=" N TRP A 890 " --> pdb=" O THR A 886 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TYR A 891 " --> pdb=" O ALA A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 902 Processing helix chain 'A' and resid 933 through 947 removed outlier: 3.508A pdb=" N CYS A 944 " --> pdb=" O TRP A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 966 Processing helix chain 'A' and resid 970 through 979 removed outlier: 3.844A pdb=" N ILE A 974 " --> pdb=" O LYS A 970 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS A 975 " --> pdb=" O PRO A 971 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A 977 " --> pdb=" O THR A 973 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU A 979 " --> pdb=" O LYS A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 989 removed outlier: 3.563A pdb=" N ILE A 988 " --> pdb=" O THR A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1003 removed outlier: 3.655A pdb=" N MET A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A1003 " --> pdb=" O PRO A 999 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 998 through 1003' Processing helix chain 'A' and resid 1009 through 1018 removed outlier: 3.575A pdb=" N ILE A1014 " --> pdb=" O LYS A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1030 removed outlier: 3.905A pdb=" N VAL A1029 " --> pdb=" O THR A1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1040 removed outlier: 3.702A pdb=" N ILE A1039 " --> pdb=" O THR A1035 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE A1040 " --> pdb=" O TRP A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1061 removed outlier: 3.627A pdb=" N ARG A1052 " --> pdb=" O GLY A1048 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 530 through 536 removed outlier: 6.283A pdb=" N ALA A 512 " --> pdb=" O ASN A 640 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ILE A 642 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE A 514 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA A 639 " --> pdb=" O ALA A 650 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ALA A 650 " --> pdb=" O ALA A 639 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE A 641 " --> pdb=" O LEU A 648 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 643 " --> pdb=" O GLN A 646 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 697 through 698 removed outlier: 4.066A pdb=" N GLN A 739 " --> pdb=" O SER A 598 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 688 through 690 Processing sheet with id=AA4, first strand: chain 'A' and resid 767 through 768 244 hydrogen bonds defined for protein. 705 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 1 stacking parallelities Total time for adding SS restraints: 1.91 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1920 1.34 - 1.46: 1360 1.46 - 1.58: 3033 1.58 - 1.69: 20 1.69 - 1.81: 34 Bond restraints: 6367 Sorted by residual: bond pdb=" CB PRO A 471 " pdb=" CG PRO A 471 " ideal model delta sigma weight residual 1.492 1.591 -0.099 5.00e-02 4.00e+02 3.94e+00 bond pdb=" CB PRO A 652 " pdb=" CG PRO A 652 " ideal model delta sigma weight residual 1.492 1.556 -0.064 5.00e-02 4.00e+02 1.66e+00 bond pdb=" C VAL A 695 " pdb=" N LYS A 696 " ideal model delta sigma weight residual 1.332 1.318 0.015 1.40e-02 5.10e+03 1.11e+00 bond pdb=" CG PRO A 471 " pdb=" CD PRO A 471 " ideal model delta sigma weight residual 1.503 1.534 -0.031 3.40e-02 8.65e+02 8.25e-01 bond pdb=" CB MET A 834 " pdb=" CG MET A 834 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.72e-01 ... (remaining 6362 not shown) Histogram of bond angle deviations from ideal: 99.61 - 106.51: 231 106.51 - 113.42: 3514 113.42 - 120.32: 2318 120.32 - 127.22: 2477 127.22 - 134.13: 103 Bond angle restraints: 8643 Sorted by residual: angle pdb=" CB MET A 834 " pdb=" CG MET A 834 " pdb=" SD MET A 834 " ideal model delta sigma weight residual 112.70 123.37 -10.67 3.00e+00 1.11e-01 1.26e+01 angle pdb=" CA MET A 908 " pdb=" CB MET A 908 " pdb=" CG MET A 908 " ideal model delta sigma weight residual 114.10 120.89 -6.79 2.00e+00 2.50e-01 1.15e+01 angle pdb=" N VAL A 564 " pdb=" CA VAL A 564 " pdb=" C VAL A 564 " ideal model delta sigma weight residual 113.10 109.89 3.21 9.70e-01 1.06e+00 1.09e+01 angle pdb=" CA PRO A 471 " pdb=" N PRO A 471 " pdb=" CD PRO A 471 " ideal model delta sigma weight residual 112.00 107.84 4.16 1.40e+00 5.10e-01 8.84e+00 angle pdb=" CA MET A 834 " pdb=" CB MET A 834 " pdb=" CG MET A 834 " ideal model delta sigma weight residual 114.10 119.55 -5.45 2.00e+00 2.50e-01 7.43e+00 ... (remaining 8638 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.16: 3487 25.16 - 50.31: 329 50.31 - 75.47: 41 75.47 - 100.62: 12 100.62 - 125.78: 1 Dihedral angle restraints: 3870 sinusoidal: 1722 harmonic: 2148 Sorted by residual: dihedral pdb=" O4' A C 11 " pdb=" C1' A C 11 " pdb=" N9 A C 11 " pdb=" C4 A C 11 " ideal model delta sinusoidal sigma weight residual 68.00 154.63 -86.63 1 1.70e+01 3.46e-03 3.13e+01 dihedral pdb=" O4' A C 9 " pdb=" C1' A C 9 " pdb=" N9 A C 9 " pdb=" C4 A C 9 " ideal model delta sinusoidal sigma weight residual 68.00 130.20 -62.20 1 1.70e+01 3.46e-03 1.77e+01 dihedral pdb=" CA MET A 908 " pdb=" C MET A 908 " pdb=" N PRO A 909 " pdb=" CA PRO A 909 " ideal model delta harmonic sigma weight residual -180.00 -159.43 -20.57 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 3867 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 569 0.028 - 0.056: 272 0.056 - 0.084: 74 0.084 - 0.111: 43 0.111 - 0.139: 8 Chirality restraints: 966 Sorted by residual: chirality pdb=" CA PRO A 909 " pdb=" N PRO A 909 " pdb=" C PRO A 909 " pdb=" CB PRO A 909 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA ILE A 802 " pdb=" N ILE A 802 " pdb=" C ILE A 802 " pdb=" CB ILE A 802 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.87e-01 chirality pdb=" CA ILE A 830 " pdb=" N ILE A 830 " pdb=" C ILE A 830 " pdb=" CB ILE A 830 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.85e-01 ... (remaining 963 not shown) Planarity restraints: 1042 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 288 " 0.017 2.00e-02 2.50e+03 1.39e-02 4.82e+00 pdb=" CG TRP A 288 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP A 288 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A 288 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 288 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 288 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 288 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 288 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 288 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 288 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 954 " 0.035 5.00e-02 4.00e+02 5.30e-02 4.50e+00 pdb=" N PRO A 955 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 955 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 955 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 470 " -0.034 5.00e-02 4.00e+02 4.97e-02 3.95e+00 pdb=" N PRO A 471 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 471 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 471 " -0.027 5.00e-02 4.00e+02 ... (remaining 1039 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 386 2.73 - 3.27: 6798 3.27 - 3.81: 10803 3.81 - 4.36: 12577 4.36 - 4.90: 20186 Nonbonded interactions: 50750 Sorted by model distance: nonbonded pdb=" OG SER A 534 " pdb=" O GLN A 659 " model vdw 2.187 2.440 nonbonded pdb=" O LYS A1017 " pdb=" OG1 THR A1021 " model vdw 2.208 2.440 nonbonded pdb=" O TRP A 899 " pdb=" OG1 THR A 902 " model vdw 2.224 2.440 nonbonded pdb=" O CYS A 661 " pdb=" OG SER A 664 " model vdw 2.227 2.440 nonbonded pdb=" O THR A 954 " pdb=" OG1 THR A 957 " model vdw 2.230 2.440 ... (remaining 50745 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 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: 3.740 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 22.090 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6592 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 : 0.003 0.099 6367 Z= 0.164 Angle : 0.571 10.665 8643 Z= 0.291 Chirality : 0.039 0.139 966 Planarity : 0.004 0.053 1042 Dihedral : 18.376 125.781 2474 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.15 % Allowed : 31.07 % Favored : 68.78 % 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: -0.09 (0.33), residues: 722 helix: 0.61 (0.31), residues: 306 sheet: -0.42 (0.90), residues: 43 loop : -0.51 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 288 HIS 0.002 0.001 HIS A 910 PHE 0.020 0.001 PHE A 651 TYR 0.005 0.001 TYR A 912 ARG 0.003 0.000 ARG A 577 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 173 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 MET cc_start: 0.3185 (mmt) cc_final: 0.2803 (mmt) REVERT: A 288 TRP cc_start: 0.7789 (t-100) cc_final: 0.7409 (t-100) REVERT: A 505 LEU cc_start: 0.7792 (mp) cc_final: 0.7453 (mp) REVERT: A 536 MET cc_start: 0.6887 (ptp) cc_final: 0.6429 (ptp) REVERT: A 538 ILE cc_start: 0.7835 (mm) cc_final: 0.7608 (mp) REVERT: A 542 ILE cc_start: 0.8443 (mt) cc_final: 0.8164 (mt) REVERT: A 560 HIS cc_start: 0.7150 (t-90) cc_final: 0.6456 (t-90) REVERT: A 573 TRP cc_start: 0.7753 (p-90) cc_final: 0.7502 (p-90) REVERT: A 627 LEU cc_start: 0.6972 (mt) cc_final: 0.6520 (mt) REVERT: A 654 LYS cc_start: 0.7311 (mmtp) cc_final: 0.6892 (mmtm) REVERT: A 666 LEU cc_start: 0.8573 (mm) cc_final: 0.8330 (mm) REVERT: A 673 GLU cc_start: 0.7564 (tm-30) cc_final: 0.6859 (tm-30) REVERT: A 680 ARG cc_start: 0.8733 (mtm-85) cc_final: 0.8443 (mtm-85) REVERT: A 710 ASN cc_start: 0.7593 (t0) cc_final: 0.7241 (p0) REVERT: A 746 ASN cc_start: 0.7794 (t0) cc_final: 0.7570 (t0) REVERT: A 759 PHE cc_start: 0.7536 (m-80) cc_final: 0.7025 (m-80) REVERT: A 764 LYS cc_start: 0.6870 (tmmt) cc_final: 0.6668 (tmtt) REVERT: A 766 ILE cc_start: 0.7469 (pt) cc_final: 0.6724 (pt) REVERT: A 772 GLN cc_start: 0.6497 (mm-40) cc_final: 0.6252 (mm110) REVERT: A 791 GLU cc_start: 0.8402 (tp30) cc_final: 0.8090 (tp30) REVERT: A 815 MET cc_start: 0.5936 (tmm) cc_final: 0.5234 (tmm) REVERT: A 823 TYR cc_start: 0.8196 (t80) cc_final: 0.7947 (t80) REVERT: A 876 LYS cc_start: 0.7527 (tptt) cc_final: 0.7320 (tptt) REVERT: A 883 VAL cc_start: 0.8772 (t) cc_final: 0.8538 (t) REVERT: A 919 LYS cc_start: 0.7805 (tmtt) cc_final: 0.7560 (ttpt) REVERT: A 986 GLN cc_start: 0.8291 (tm-30) cc_final: 0.8036 (pp30) REVERT: A 997 LYS cc_start: 0.7507 (ttmm) cc_final: 0.7254 (mtmt) REVERT: A 1055 ASN cc_start: 0.7381 (t0) cc_final: 0.6801 (t0) REVERT: A 1059 GLN cc_start: 0.8287 (mm-40) cc_final: 0.8040 (mm-40) outliers start: 1 outliers final: 0 residues processed: 174 average time/residue: 0.2100 time to fit residues: 46.1391 Evaluate side-chains 147 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 66 optimal weight: 0.1980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN ** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 ASN ** A 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 618 ASN ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 ASN A 826 ASN A 898 GLN ** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1030 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6367 Z= 0.209 Angle : 0.615 7.187 8643 Z= 0.319 Chirality : 0.042 0.158 966 Planarity : 0.004 0.049 1042 Dihedral : 10.104 122.244 898 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 5.43 % Allowed : 27.90 % Favored : 66.67 % 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: -0.32 (0.33), residues: 722 helix: 0.35 (0.28), residues: 358 sheet: -1.02 (0.84), residues: 43 loop : -0.63 (0.39), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 288 HIS 0.003 0.001 HIS A 585 PHE 0.014 0.001 PHE A 781 TYR 0.010 0.001 TYR A1054 ARG 0.003 0.001 ARG A 809 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 158 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 MET cc_start: 0.3250 (mmt) cc_final: 0.3003 (mmt) REVERT: A 491 PHE cc_start: 0.8858 (OUTLIER) cc_final: 0.8641 (m-80) REVERT: A 505 LEU cc_start: 0.7802 (mp) cc_final: 0.7553 (mp) REVERT: A 536 MET cc_start: 0.6886 (ptp) cc_final: 0.6584 (ptp) REVERT: A 538 ILE cc_start: 0.7792 (mm) cc_final: 0.7443 (mp) REVERT: A 552 GLN cc_start: 0.7557 (tp-100) cc_final: 0.7205 (mt0) REVERT: A 560 HIS cc_start: 0.7279 (t-90) cc_final: 0.6557 (t-90) REVERT: A 563 GLN cc_start: 0.7737 (tm-30) cc_final: 0.7430 (tm-30) REVERT: A 627 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.7055 (mt) REVERT: A 654 LYS cc_start: 0.7313 (mmtp) cc_final: 0.6997 (mmtt) REVERT: A 666 LEU cc_start: 0.8702 (mm) cc_final: 0.8407 (mm) REVERT: A 673 GLU cc_start: 0.7652 (tm-30) cc_final: 0.6875 (tm-30) REVERT: A 681 GLN cc_start: 0.8221 (mm110) cc_final: 0.7981 (mm-40) REVERT: A 710 ASN cc_start: 0.7634 (t0) cc_final: 0.7245 (p0) REVERT: A 759 PHE cc_start: 0.7700 (m-80) cc_final: 0.7207 (m-80) REVERT: A 766 ILE cc_start: 0.7346 (pt) cc_final: 0.6932 (pt) REVERT: A 772 GLN cc_start: 0.6860 (mm-40) cc_final: 0.6507 (mm-40) REVERT: A 785 TYR cc_start: 0.7887 (m-80) cc_final: 0.7417 (m-80) REVERT: A 789 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7391 (pp) REVERT: A 790 LYS cc_start: 0.8819 (ptpp) cc_final: 0.8145 (ptpp) REVERT: A 793 LYS cc_start: 0.8925 (mttt) cc_final: 0.8361 (mttt) REVERT: A 815 MET cc_start: 0.6026 (tmm) cc_final: 0.5277 (tmm) REVERT: A 823 TYR cc_start: 0.8157 (t80) cc_final: 0.7846 (t80) REVERT: A 834 MET cc_start: 0.7256 (tmm) cc_final: 0.6984 (tmm) REVERT: A 837 PHE cc_start: 0.8108 (m-80) cc_final: 0.7851 (m-80) REVERT: A 876 LYS cc_start: 0.7754 (tptt) cc_final: 0.7470 (tptt) REVERT: A 919 LYS cc_start: 0.7969 (tmtt) cc_final: 0.7586 (ttpt) REVERT: A 997 LYS cc_start: 0.7507 (ttmm) cc_final: 0.7303 (mtmt) REVERT: A 1058 LYS cc_start: 0.8324 (ttmm) cc_final: 0.7999 (ttmm) outliers start: 36 outliers final: 20 residues processed: 182 average time/residue: 0.2054 time to fit residues: 47.5341 Evaluate side-chains 176 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 153 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 491 PHE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 581 ASN Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 800 LYS Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 898 GLN Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1031 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 36 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 59 optimal weight: 0.0070 chunk 65 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 overall best weight: 0.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 669 ASN ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 GLN ** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1055 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6367 Z= 0.205 Angle : 0.603 6.864 8643 Z= 0.312 Chirality : 0.042 0.167 966 Planarity : 0.004 0.048 1042 Dihedral : 10.026 116.522 898 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 5.58 % Allowed : 28.36 % Favored : 66.06 % 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: -0.48 (0.32), residues: 722 helix: 0.29 (0.28), residues: 365 sheet: -1.20 (0.81), residues: 43 loop : -0.82 (0.38), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 573 HIS 0.006 0.001 HIS A 585 PHE 0.017 0.001 PHE A 781 TYR 0.009 0.001 TYR A1054 ARG 0.008 0.001 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 175 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 MET cc_start: 0.3394 (mmt) cc_final: 0.3134 (mmt) REVERT: A 285 GLN cc_start: 0.6908 (mp10) cc_final: 0.6696 (mp10) REVERT: A 288 TRP cc_start: 0.8292 (t-100) cc_final: 0.7937 (t-100) REVERT: A 292 LYS cc_start: 0.8740 (mttp) cc_final: 0.8499 (mttp) REVERT: A 443 GLN cc_start: 0.8745 (tm-30) cc_final: 0.8480 (tm-30) REVERT: A 463 ASN cc_start: 0.8153 (m-40) cc_final: 0.7946 (m-40) REVERT: A 495 LEU cc_start: 0.7244 (tt) cc_final: 0.7031 (tp) REVERT: A 505 LEU cc_start: 0.7865 (mp) cc_final: 0.7607 (mp) REVERT: A 536 MET cc_start: 0.6956 (ptp) cc_final: 0.6667 (ptp) REVERT: A 538 ILE cc_start: 0.7759 (mm) cc_final: 0.7513 (mp) REVERT: A 545 LYS cc_start: 0.8538 (tttt) cc_final: 0.8280 (mttt) REVERT: A 560 HIS cc_start: 0.7357 (t-90) cc_final: 0.6619 (t-90) REVERT: A 578 LYS cc_start: 0.7756 (tttm) cc_final: 0.7263 (tttp) REVERT: A 597 ILE cc_start: 0.7493 (mp) cc_final: 0.7012 (mm) REVERT: A 617 LEU cc_start: 0.5559 (OUTLIER) cc_final: 0.5256 (tp) REVERT: A 627 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7108 (mt) REVERT: A 651 PHE cc_start: 0.7417 (p90) cc_final: 0.6725 (p90) REVERT: A 654 LYS cc_start: 0.7371 (mmtp) cc_final: 0.7056 (mmtt) REVERT: A 666 LEU cc_start: 0.8715 (mm) cc_final: 0.8395 (mt) REVERT: A 667 LEU cc_start: 0.8901 (mt) cc_final: 0.8695 (mt) REVERT: A 673 GLU cc_start: 0.7678 (tm-30) cc_final: 0.6890 (tm-30) REVERT: A 681 GLN cc_start: 0.8273 (mm110) cc_final: 0.8071 (mm110) REVERT: A 699 LEU cc_start: 0.7784 (mp) cc_final: 0.7540 (mp) REVERT: A 710 ASN cc_start: 0.7602 (t0) cc_final: 0.7171 (p0) REVERT: A 759 PHE cc_start: 0.7737 (m-80) cc_final: 0.7363 (t80) REVERT: A 766 ILE cc_start: 0.7330 (pt) cc_final: 0.6888 (pt) REVERT: A 772 GLN cc_start: 0.6908 (mm-40) cc_final: 0.6323 (mm110) REVERT: A 789 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7430 (pp) REVERT: A 790 LYS cc_start: 0.8838 (ptpp) cc_final: 0.8225 (ptpp) REVERT: A 793 LYS cc_start: 0.8916 (mttt) cc_final: 0.8343 (mttt) REVERT: A 815 MET cc_start: 0.6061 (tmm) cc_final: 0.5307 (tmm) REVERT: A 823 TYR cc_start: 0.8156 (t80) cc_final: 0.7828 (t80) REVERT: A 834 MET cc_start: 0.7241 (tmm) cc_final: 0.6874 (tmm) REVERT: A 876 LYS cc_start: 0.7822 (tptt) cc_final: 0.7602 (tptt) REVERT: A 898 GLN cc_start: 0.7143 (OUTLIER) cc_final: 0.6677 (tt0) REVERT: A 919 LYS cc_start: 0.8005 (tmtt) cc_final: 0.7611 (ttpt) REVERT: A 939 ASN cc_start: 0.7199 (OUTLIER) cc_final: 0.6385 (m-40) REVERT: A 1047 LYS cc_start: 0.7578 (tttt) cc_final: 0.7261 (tttp) outliers start: 37 outliers final: 20 residues processed: 197 average time/residue: 0.2115 time to fit residues: 52.6266 Evaluate side-chains 199 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 174 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 619 LYS Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 800 LYS Chi-restraints excluded: chain A residue 810 ILE Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 898 GLN Chi-restraints excluded: chain A residue 908 MET Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 939 ASN Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 990 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 0.3980 chunk 49 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 63 optimal weight: 0.0970 chunk 19 optimal weight: 0.5980 chunk 58 optimal weight: 0.0070 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN ** A 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 669 ASN ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 898 GLN ** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 6367 Z= 0.164 Angle : 0.572 7.219 8643 Z= 0.288 Chirality : 0.040 0.152 966 Planarity : 0.004 0.049 1042 Dihedral : 9.755 108.718 898 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 18.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.98 % Allowed : 28.36 % Favored : 66.67 % 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: -0.37 (0.32), residues: 722 helix: 0.50 (0.28), residues: 358 sheet: -1.28 (0.80), residues: 43 loop : -0.87 (0.37), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 288 HIS 0.007 0.001 HIS A 585 PHE 0.012 0.001 PHE A 781 TYR 0.022 0.001 TYR A 414 ARG 0.003 0.000 ARG A 680 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 175 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 MET cc_start: 0.3281 (mmt) cc_final: 0.3044 (mmt) REVERT: A 288 TRP cc_start: 0.8314 (t-100) cc_final: 0.7825 (t-100) REVERT: A 292 LYS cc_start: 0.8774 (mttp) cc_final: 0.8432 (mttp) REVERT: A 428 GLU cc_start: 0.7424 (mp0) cc_final: 0.7004 (mp0) REVERT: A 479 GLU cc_start: 0.6680 (tp30) cc_final: 0.6438 (tp30) REVERT: A 495 LEU cc_start: 0.7226 (tt) cc_final: 0.7020 (tp) REVERT: A 505 LEU cc_start: 0.7871 (mp) cc_final: 0.7582 (mp) REVERT: A 536 MET cc_start: 0.6918 (ptp) cc_final: 0.6663 (ptp) REVERT: A 538 ILE cc_start: 0.7732 (mm) cc_final: 0.7491 (mp) REVERT: A 545 LYS cc_start: 0.8434 (tttt) cc_final: 0.8075 (mttt) REVERT: A 560 HIS cc_start: 0.7376 (t-90) cc_final: 0.6596 (t-90) REVERT: A 578 LYS cc_start: 0.7787 (tttm) cc_final: 0.7243 (tttp) REVERT: A 597 ILE cc_start: 0.7475 (mp) cc_final: 0.7074 (mm) REVERT: A 607 LYS cc_start: 0.7071 (ptpt) cc_final: 0.6289 (tmmt) REVERT: A 617 LEU cc_start: 0.5531 (OUTLIER) cc_final: 0.5280 (tp) REVERT: A 651 PHE cc_start: 0.7419 (p90) cc_final: 0.6728 (p90) REVERT: A 654 LYS cc_start: 0.7385 (mmtp) cc_final: 0.7071 (mmtm) REVERT: A 666 LEU cc_start: 0.8620 (mm) cc_final: 0.8389 (mm) REVERT: A 667 LEU cc_start: 0.8864 (mt) cc_final: 0.8650 (mt) REVERT: A 672 LEU cc_start: 0.8399 (mm) cc_final: 0.8019 (mm) REVERT: A 673 GLU cc_start: 0.7668 (tm-30) cc_final: 0.6869 (tm-30) REVERT: A 710 ASN cc_start: 0.7551 (t0) cc_final: 0.7139 (p0) REVERT: A 720 LYS cc_start: 0.8572 (mtmm) cc_final: 0.8349 (mtmm) REVERT: A 742 LEU cc_start: 0.8233 (tp) cc_final: 0.7968 (mp) REVERT: A 766 ILE cc_start: 0.7363 (pt) cc_final: 0.6947 (pt) REVERT: A 772 GLN cc_start: 0.6791 (mm-40) cc_final: 0.6302 (mm110) REVERT: A 790 LYS cc_start: 0.8842 (ptpp) cc_final: 0.8338 (ptpp) REVERT: A 793 LYS cc_start: 0.8919 (mttt) cc_final: 0.8349 (mttt) REVERT: A 815 MET cc_start: 0.6042 (tmm) cc_final: 0.5265 (tmm) REVERT: A 823 TYR cc_start: 0.8050 (t80) cc_final: 0.7799 (t80) REVERT: A 834 MET cc_start: 0.7234 (tmm) cc_final: 0.6808 (tmm) REVERT: A 876 LYS cc_start: 0.7799 (tptt) cc_final: 0.7583 (tptt) REVERT: A 880 LYS cc_start: 0.7503 (ttmm) cc_final: 0.7046 (mmtt) REVERT: A 883 VAL cc_start: 0.8804 (t) cc_final: 0.8326 (p) REVERT: A 890 TRP cc_start: 0.6967 (OUTLIER) cc_final: 0.6406 (m100) REVERT: A 939 ASN cc_start: 0.7112 (OUTLIER) cc_final: 0.5776 (t0) outliers start: 33 outliers final: 23 residues processed: 194 average time/residue: 0.2129 time to fit residues: 52.3316 Evaluate side-chains 196 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 170 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 619 LYS Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain A residue 800 LYS Chi-restraints excluded: chain A residue 810 ILE Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 890 TRP Chi-restraints excluded: chain A residue 898 GLN Chi-restraints excluded: chain A residue 908 MET Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 939 ASN Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 990 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 40 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 52 optimal weight: 20.0000 chunk 29 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 48 optimal weight: 0.1980 chunk 0 optimal weight: 50.0000 chunk 36 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 898 GLN A 925 GLN ** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6367 Z= 0.249 Angle : 0.627 7.066 8643 Z= 0.319 Chirality : 0.043 0.156 966 Planarity : 0.004 0.043 1042 Dihedral : 9.676 96.493 898 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 21.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 6.03 % Allowed : 27.60 % Favored : 66.37 % 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: -0.52 (0.32), residues: 722 helix: 0.40 (0.28), residues: 356 sheet: -1.63 (0.75), residues: 43 loop : -0.93 (0.37), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 288 HIS 0.008 0.001 HIS A 585 PHE 0.013 0.002 PHE A 759 TYR 0.016 0.001 TYR A 414 ARG 0.004 0.000 ARG A 680 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 165 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 MET cc_start: 0.3713 (mmt) cc_final: 0.3429 (mmt) REVERT: A 443 GLN cc_start: 0.8849 (tm-30) cc_final: 0.7851 (tm-30) REVERT: A 447 GLU cc_start: 0.8859 (tt0) cc_final: 0.8184 (mt-10) REVERT: A 479 GLU cc_start: 0.6760 (tp30) cc_final: 0.6494 (tp30) REVERT: A 505 LEU cc_start: 0.7878 (mp) cc_final: 0.7493 (mp) REVERT: A 510 TYR cc_start: 0.6598 (m-80) cc_final: 0.6212 (m-80) REVERT: A 536 MET cc_start: 0.6930 (ptp) cc_final: 0.6623 (ptp) REVERT: A 538 ILE cc_start: 0.7763 (mm) cc_final: 0.7536 (mp) REVERT: A 545 LYS cc_start: 0.8484 (tttt) cc_final: 0.8165 (mtpt) REVERT: A 560 HIS cc_start: 0.7490 (t-90) cc_final: 0.6552 (t70) REVERT: A 578 LYS cc_start: 0.7814 (tttm) cc_final: 0.7389 (tttp) REVERT: A 597 ILE cc_start: 0.7517 (mp) cc_final: 0.7256 (mp) REVERT: A 617 LEU cc_start: 0.5500 (OUTLIER) cc_final: 0.5288 (tp) REVERT: A 631 ARG cc_start: 0.7229 (ttm-80) cc_final: 0.7012 (ttp80) REVERT: A 666 LEU cc_start: 0.8729 (mm) cc_final: 0.8135 (mm) REVERT: A 667 LEU cc_start: 0.8965 (mt) cc_final: 0.8670 (mt) REVERT: A 668 PHE cc_start: 0.8947 (t80) cc_final: 0.8707 (t80) REVERT: A 669 ASN cc_start: 0.8919 (m-40) cc_final: 0.8416 (m110) REVERT: A 672 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8038 (mm) REVERT: A 673 GLU cc_start: 0.7792 (tm-30) cc_final: 0.6993 (tm-30) REVERT: A 681 GLN cc_start: 0.8341 (mm110) cc_final: 0.8079 (mm-40) REVERT: A 710 ASN cc_start: 0.7538 (t0) cc_final: 0.7315 (t0) REVERT: A 720 LYS cc_start: 0.8602 (mtmm) cc_final: 0.8387 (mtmm) REVERT: A 742 LEU cc_start: 0.8349 (tp) cc_final: 0.8063 (mp) REVERT: A 789 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7474 (pp) REVERT: A 790 LYS cc_start: 0.8904 (ptpp) cc_final: 0.8231 (ptpp) REVERT: A 793 LYS cc_start: 0.8991 (mttt) cc_final: 0.8442 (mttt) REVERT: A 815 MET cc_start: 0.6156 (tmm) cc_final: 0.5379 (tmm) REVERT: A 823 TYR cc_start: 0.8108 (t80) cc_final: 0.7906 (t80) REVERT: A 834 MET cc_start: 0.7289 (tmm) cc_final: 0.6882 (tmm) REVERT: A 876 LYS cc_start: 0.7901 (tptt) cc_final: 0.7695 (tptt) REVERT: A 883 VAL cc_start: 0.8781 (t) cc_final: 0.8398 (p) REVERT: A 890 TRP cc_start: 0.7032 (OUTLIER) cc_final: 0.6618 (m100) REVERT: A 919 LYS cc_start: 0.8055 (tmtt) cc_final: 0.7657 (ttpt) REVERT: A 939 ASN cc_start: 0.7235 (OUTLIER) cc_final: 0.6368 (m-40) REVERT: A 997 LYS cc_start: 0.7062 (mtmt) cc_final: 0.6733 (mtmm) REVERT: A 1058 LYS cc_start: 0.7904 (tppt) cc_final: 0.7563 (ttmm) REVERT: A 1059 GLN cc_start: 0.7571 (pt0) cc_final: 0.7350 (pp30) outliers start: 40 outliers final: 27 residues processed: 189 average time/residue: 0.2118 time to fit residues: 50.8044 Evaluate side-chains 190 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 158 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 619 LYS Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain A residue 800 LYS Chi-restraints excluded: chain A residue 810 ILE Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 890 TRP Chi-restraints excluded: chain A residue 898 GLN Chi-restraints excluded: chain A residue 908 MET Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 939 ASN Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 1035 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 63 optimal weight: 0.9980 chunk 13 optimal weight: 0.0020 chunk 41 optimal weight: 0.0270 chunk 17 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 5 optimal weight: 10.0000 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 0.0970 chunk 68 optimal weight: 5.9990 overall best weight: 0.2844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 GLN ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 898 GLN ** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6367 Z= 0.170 Angle : 0.608 10.968 8643 Z= 0.297 Chirality : 0.041 0.157 966 Planarity : 0.004 0.048 1042 Dihedral : 9.436 91.338 898 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.98 % Allowed : 30.17 % Favored : 64.86 % 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: -0.45 (0.32), residues: 722 helix: 0.40 (0.28), residues: 361 sheet: -1.57 (0.76), residues: 43 loop : -0.83 (0.37), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 888 HIS 0.003 0.001 HIS A 585 PHE 0.020 0.001 PHE A 836 TYR 0.010 0.001 TYR A 414 ARG 0.003 0.000 ARG A 747 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 167 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 MET cc_start: 0.3522 (mmt) cc_final: 0.3264 (mmt) REVERT: A 479 GLU cc_start: 0.6821 (tp30) cc_final: 0.6479 (tp30) REVERT: A 505 LEU cc_start: 0.7850 (mp) cc_final: 0.7536 (mp) REVERT: A 531 ARG cc_start: 0.2667 (tpt170) cc_final: 0.1734 (tpt170) REVERT: A 536 MET cc_start: 0.6924 (ptp) cc_final: 0.6662 (ptp) REVERT: A 538 ILE cc_start: 0.7733 (mm) cc_final: 0.7495 (mp) REVERT: A 578 LYS cc_start: 0.7742 (tttm) cc_final: 0.7498 (ttmm) REVERT: A 607 LYS cc_start: 0.8018 (tptt) cc_final: 0.7318 (ttpt) REVERT: A 617 LEU cc_start: 0.5535 (OUTLIER) cc_final: 0.5296 (tp) REVERT: A 666 LEU cc_start: 0.8649 (mm) cc_final: 0.8329 (mm) REVERT: A 667 LEU cc_start: 0.8883 (mt) cc_final: 0.8646 (mt) REVERT: A 668 PHE cc_start: 0.8890 (t80) cc_final: 0.8679 (t80) REVERT: A 672 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7992 (mm) REVERT: A 673 GLU cc_start: 0.7685 (tm-30) cc_final: 0.6939 (tm-30) REVERT: A 681 GLN cc_start: 0.8265 (mm110) cc_final: 0.8002 (mm-40) REVERT: A 705 ILE cc_start: 0.7123 (mt) cc_final: 0.6675 (pt) REVERT: A 710 ASN cc_start: 0.7504 (t0) cc_final: 0.7276 (t0) REVERT: A 742 LEU cc_start: 0.8272 (tp) cc_final: 0.8016 (mp) REVERT: A 790 LYS cc_start: 0.8816 (ptpp) cc_final: 0.8260 (ptpp) REVERT: A 793 LYS cc_start: 0.8960 (mttt) cc_final: 0.8412 (mttt) REVERT: A 815 MET cc_start: 0.6116 (tmm) cc_final: 0.5334 (tmm) REVERT: A 820 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8168 (tptt) REVERT: A 823 TYR cc_start: 0.8043 (t80) cc_final: 0.7822 (t80) REVERT: A 834 MET cc_start: 0.7289 (tmm) cc_final: 0.6825 (tmm) REVERT: A 876 LYS cc_start: 0.7848 (tptt) cc_final: 0.7646 (tptt) REVERT: A 883 VAL cc_start: 0.8777 (t) cc_final: 0.8377 (p) REVERT: A 888 TRP cc_start: 0.7881 (t60) cc_final: 0.6363 (t60) REVERT: A 890 TRP cc_start: 0.6960 (OUTLIER) cc_final: 0.6513 (m100) REVERT: A 919 LYS cc_start: 0.7994 (tmtt) cc_final: 0.7632 (ttpt) REVERT: A 939 ASN cc_start: 0.7103 (OUTLIER) cc_final: 0.6208 (m-40) REVERT: A 1040 PHE cc_start: 0.7549 (m-80) cc_final: 0.7320 (m-80) REVERT: A 1046 ASP cc_start: 0.7585 (p0) cc_final: 0.6953 (p0) REVERT: A 1058 LYS cc_start: 0.8019 (tppt) cc_final: 0.7681 (ttmm) REVERT: A 1059 GLN cc_start: 0.7624 (pt0) cc_final: 0.7372 (pp30) outliers start: 33 outliers final: 24 residues processed: 182 average time/residue: 0.2122 time to fit residues: 49.4356 Evaluate side-chains 189 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 160 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 288 TRP Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 619 LYS Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain A residue 810 ILE Chi-restraints excluded: chain A residue 820 LYS Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 890 TRP Chi-restraints excluded: chain A residue 898 GLN Chi-restraints excluded: chain A residue 908 MET Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 939 ASN Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 1035 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 7 optimal weight: 0.5980 chunk 40 optimal weight: 5.9990 chunk 51 optimal weight: 0.0870 chunk 39 optimal weight: 2.9990 chunk 59 optimal weight: 0.2980 chunk 70 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 669 ASN ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 898 GLN ** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6367 Z= 0.183 Angle : 0.612 10.585 8643 Z= 0.302 Chirality : 0.041 0.306 966 Planarity : 0.004 0.048 1042 Dihedral : 9.306 88.230 898 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 19.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 5.28 % Allowed : 30.02 % Favored : 64.71 % 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: -0.47 (0.33), residues: 722 helix: 0.37 (0.28), residues: 368 sheet: -1.55 (0.76), residues: 43 loop : -0.86 (0.38), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 888 HIS 0.003 0.001 HIS A 585 PHE 0.011 0.001 PHE A 291 TYR 0.011 0.001 TYR A 414 ARG 0.007 0.000 ARG A 631 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 155 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 MET cc_start: 0.3752 (mmt) cc_final: 0.3452 (mmt) REVERT: A 479 GLU cc_start: 0.6811 (tp30) cc_final: 0.6409 (tp30) REVERT: A 505 LEU cc_start: 0.7846 (mp) cc_final: 0.7551 (mp) REVERT: A 536 MET cc_start: 0.6954 (ptp) cc_final: 0.6704 (ptp) REVERT: A 538 ILE cc_start: 0.7717 (mm) cc_final: 0.7481 (mp) REVERT: A 560 HIS cc_start: 0.7499 (t-90) cc_final: 0.6595 (t-90) REVERT: A 578 LYS cc_start: 0.7757 (tttm) cc_final: 0.7321 (tttp) REVERT: A 607 LYS cc_start: 0.8007 (tptt) cc_final: 0.7275 (ttpt) REVERT: A 617 LEU cc_start: 0.5581 (OUTLIER) cc_final: 0.5245 (tp) REVERT: A 651 PHE cc_start: 0.7254 (p90) cc_final: 0.6557 (p90) REVERT: A 666 LEU cc_start: 0.8665 (mm) cc_final: 0.8421 (mm) REVERT: A 667 LEU cc_start: 0.8900 (mt) cc_final: 0.8653 (mt) REVERT: A 672 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7989 (mm) REVERT: A 673 GLU cc_start: 0.7717 (tm-30) cc_final: 0.6994 (tm-30) REVERT: A 681 GLN cc_start: 0.8249 (mm110) cc_final: 0.7995 (mm-40) REVERT: A 705 ILE cc_start: 0.7123 (mt) cc_final: 0.6658 (pt) REVERT: A 710 ASN cc_start: 0.7484 (t0) cc_final: 0.7262 (t0) REVERT: A 742 LEU cc_start: 0.8330 (tp) cc_final: 0.8076 (mp) REVERT: A 759 PHE cc_start: 0.7822 (m-80) cc_final: 0.7389 (t80) REVERT: A 790 LYS cc_start: 0.8813 (ptpp) cc_final: 0.8290 (ptpp) REVERT: A 793 LYS cc_start: 0.8979 (mttt) cc_final: 0.8428 (mttt) REVERT: A 815 MET cc_start: 0.6138 (tmm) cc_final: 0.5356 (tmm) REVERT: A 820 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8168 (tptt) REVERT: A 823 TYR cc_start: 0.8128 (t80) cc_final: 0.7876 (t80) REVERT: A 834 MET cc_start: 0.7305 (tmm) cc_final: 0.6806 (tmm) REVERT: A 876 LYS cc_start: 0.7877 (tptt) cc_final: 0.7664 (tptt) REVERT: A 883 VAL cc_start: 0.8731 (t) cc_final: 0.8276 (p) REVERT: A 890 TRP cc_start: 0.6941 (OUTLIER) cc_final: 0.6537 (m100) REVERT: A 919 LYS cc_start: 0.7993 (tmtt) cc_final: 0.7586 (ttpt) REVERT: A 939 ASN cc_start: 0.7144 (OUTLIER) cc_final: 0.6080 (t0) REVERT: A 1028 ARG cc_start: 0.8254 (mmm-85) cc_final: 0.8015 (tpp80) REVERT: A 1040 PHE cc_start: 0.7595 (m-80) cc_final: 0.7321 (m-80) REVERT: A 1047 LYS cc_start: 0.7767 (tttt) cc_final: 0.7417 (tttp) REVERT: A 1058 LYS cc_start: 0.8013 (tppt) cc_final: 0.7709 (ttmm) outliers start: 35 outliers final: 24 residues processed: 175 average time/residue: 0.2172 time to fit residues: 48.1427 Evaluate side-chains 179 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 150 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 288 TRP Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain A residue 800 LYS Chi-restraints excluded: chain A residue 810 ILE Chi-restraints excluded: chain A residue 820 LYS Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 890 TRP Chi-restraints excluded: chain A residue 894 ARG Chi-restraints excluded: chain A residue 898 GLN Chi-restraints excluded: chain A residue 908 MET Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 939 ASN Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 1035 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 42 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 13 optimal weight: 0.1980 chunk 44 optimal weight: 0.8980 chunk 47 optimal weight: 0.0060 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.0270 chunk 55 optimal weight: 0.0770 chunk 64 optimal weight: 1.9990 chunk 67 optimal weight: 0.0970 chunk 61 optimal weight: 0.7980 overall best weight: 0.0810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 898 GLN ** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6367 Z= 0.167 Angle : 0.615 10.102 8643 Z= 0.303 Chirality : 0.040 0.244 966 Planarity : 0.004 0.051 1042 Dihedral : 9.114 87.790 898 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.52 % Allowed : 30.62 % Favored : 64.86 % 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: -0.40 (0.33), residues: 722 helix: 0.44 (0.29), residues: 362 sheet: -1.57 (0.77), residues: 43 loop : -0.80 (0.38), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 573 HIS 0.002 0.000 HIS A 585 PHE 0.013 0.001 PHE A 291 TYR 0.009 0.001 TYR A 414 ARG 0.008 0.000 ARG A 631 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 158 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 MET cc_start: 0.3619 (mmt) cc_final: 0.3331 (mmt) REVERT: A 479 GLU cc_start: 0.6794 (tp30) cc_final: 0.6368 (tp30) REVERT: A 505 LEU cc_start: 0.7860 (mp) cc_final: 0.7586 (mp) REVERT: A 536 MET cc_start: 0.6833 (ptp) cc_final: 0.6568 (ptp) REVERT: A 538 ILE cc_start: 0.7687 (mm) cc_final: 0.7450 (mp) REVERT: A 573 TRP cc_start: 0.7871 (p-90) cc_final: 0.7598 (p-90) REVERT: A 578 LYS cc_start: 0.7699 (tttm) cc_final: 0.7296 (tttp) REVERT: A 607 LYS cc_start: 0.7983 (tptt) cc_final: 0.7291 (ttpt) REVERT: A 617 LEU cc_start: 0.5404 (OUTLIER) cc_final: 0.5085 (tp) REVERT: A 666 LEU cc_start: 0.8587 (mm) cc_final: 0.8344 (mm) REVERT: A 667 LEU cc_start: 0.8856 (mt) cc_final: 0.8539 (mt) REVERT: A 672 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7927 (mm) REVERT: A 673 GLU cc_start: 0.7683 (tm-30) cc_final: 0.6989 (tm-30) REVERT: A 705 ILE cc_start: 0.7115 (mt) cc_final: 0.6586 (pt) REVERT: A 710 ASN cc_start: 0.7504 (t0) cc_final: 0.7285 (t0) REVERT: A 742 LEU cc_start: 0.8312 (tp) cc_final: 0.8084 (mp) REVERT: A 759 PHE cc_start: 0.7633 (m-80) cc_final: 0.7353 (t80) REVERT: A 793 LYS cc_start: 0.8975 (mttt) cc_final: 0.8429 (mttt) REVERT: A 815 MET cc_start: 0.6071 (tmm) cc_final: 0.5290 (tmm) REVERT: A 820 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8168 (tptt) REVERT: A 834 MET cc_start: 0.7269 (tmm) cc_final: 0.6753 (tmm) REVERT: A 876 LYS cc_start: 0.7827 (tptt) cc_final: 0.7625 (tptt) REVERT: A 888 TRP cc_start: 0.7874 (t60) cc_final: 0.6674 (t60) REVERT: A 890 TRP cc_start: 0.6963 (OUTLIER) cc_final: 0.6505 (m100) REVERT: A 919 LYS cc_start: 0.7940 (tmtt) cc_final: 0.7635 (tttt) REVERT: A 939 ASN cc_start: 0.7019 (OUTLIER) cc_final: 0.6002 (t0) REVERT: A 1028 ARG cc_start: 0.8192 (mmm-85) cc_final: 0.7961 (tpp80) REVERT: A 1046 ASP cc_start: 0.7716 (p0) cc_final: 0.7369 (p0) REVERT: A 1047 LYS cc_start: 0.7809 (tttt) cc_final: 0.7441 (tttp) REVERT: A 1058 LYS cc_start: 0.8061 (tppt) cc_final: 0.7633 (mttt) REVERT: A 1059 GLN cc_start: 0.7143 (OUTLIER) cc_final: 0.6891 (pp30) outliers start: 30 outliers final: 22 residues processed: 174 average time/residue: 0.2082 time to fit residues: 45.9830 Evaluate side-chains 184 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 156 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 288 TRP Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain A residue 800 LYS Chi-restraints excluded: chain A residue 810 ILE Chi-restraints excluded: chain A residue 820 LYS Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 890 TRP Chi-restraints excluded: chain A residue 908 MET Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 939 ASN Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 1035 THR Chi-restraints excluded: chain A residue 1059 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 59 optimal weight: 0.0000 chunk 62 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6367 Z= 0.213 Angle : 0.643 9.601 8643 Z= 0.320 Chirality : 0.042 0.255 966 Planarity : 0.004 0.046 1042 Dihedral : 9.137 87.184 898 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.07 % Allowed : 31.83 % Favored : 64.10 % 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: -0.46 (0.32), residues: 722 helix: 0.36 (0.28), residues: 364 sheet: -1.71 (0.75), residues: 43 loop : -0.77 (0.38), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 888 HIS 0.002 0.001 HIS A 585 PHE 0.009 0.001 PHE A 917 TYR 0.011 0.001 TYR A 823 ARG 0.007 0.001 ARG A 680 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 159 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 GLU cc_start: 0.6867 (tp30) cc_final: 0.6410 (tp30) REVERT: A 505 LEU cc_start: 0.7859 (mp) cc_final: 0.7599 (mp) REVERT: A 536 MET cc_start: 0.6872 (ptp) cc_final: 0.6594 (ptp) REVERT: A 538 ILE cc_start: 0.7730 (mm) cc_final: 0.7504 (mp) REVERT: A 560 HIS cc_start: 0.7509 (t-90) cc_final: 0.6879 (t-90) REVERT: A 607 LYS cc_start: 0.7984 (tptt) cc_final: 0.7673 (tppt) REVERT: A 617 LEU cc_start: 0.5550 (OUTLIER) cc_final: 0.5284 (tp) REVERT: A 651 PHE cc_start: 0.7217 (p90) cc_final: 0.6527 (p90) REVERT: A 666 LEU cc_start: 0.8676 (mm) cc_final: 0.8338 (mm) REVERT: A 667 LEU cc_start: 0.8930 (mt) cc_final: 0.8691 (mt) REVERT: A 669 ASN cc_start: 0.8954 (m-40) cc_final: 0.8706 (m110) REVERT: A 672 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7984 (mm) REVERT: A 673 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7048 (tm-30) REVERT: A 681 GLN cc_start: 0.8212 (mm110) cc_final: 0.7995 (mm-40) REVERT: A 705 ILE cc_start: 0.7141 (mt) cc_final: 0.6620 (pt) REVERT: A 710 ASN cc_start: 0.7504 (t0) cc_final: 0.7256 (t0) REVERT: A 742 LEU cc_start: 0.8262 (tp) cc_final: 0.8024 (mp) REVERT: A 759 PHE cc_start: 0.7849 (m-80) cc_final: 0.7380 (t80) REVERT: A 793 LYS cc_start: 0.9000 (mttt) cc_final: 0.8455 (mttt) REVERT: A 815 MET cc_start: 0.6126 (tmm) cc_final: 0.5339 (tmm) REVERT: A 834 MET cc_start: 0.7318 (tmm) cc_final: 0.6791 (tmm) REVERT: A 876 LYS cc_start: 0.7879 (tptt) cc_final: 0.7662 (tptt) REVERT: A 890 TRP cc_start: 0.6957 (OUTLIER) cc_final: 0.6521 (m100) REVERT: A 919 LYS cc_start: 0.7956 (tmtt) cc_final: 0.7601 (ttpt) REVERT: A 939 ASN cc_start: 0.7173 (OUTLIER) cc_final: 0.6182 (t0) REVERT: A 1028 ARG cc_start: 0.8256 (mmm-85) cc_final: 0.8016 (tpp80) REVERT: A 1040 PHE cc_start: 0.7625 (m-80) cc_final: 0.7376 (m-80) REVERT: A 1047 LYS cc_start: 0.7819 (tttt) cc_final: 0.7434 (tttp) REVERT: A 1059 GLN cc_start: 0.7286 (pp30) cc_final: 0.7001 (pp30) outliers start: 27 outliers final: 22 residues processed: 173 average time/residue: 0.2283 time to fit residues: 50.3083 Evaluate side-chains 182 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 156 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 288 TRP Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain A residue 800 LYS Chi-restraints excluded: chain A residue 810 ILE Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 890 TRP Chi-restraints excluded: chain A residue 898 GLN Chi-restraints excluded: chain A residue 908 MET Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 939 ASN Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 1035 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 32 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 57 optimal weight: 0.5980 chunk 6 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 46 optimal weight: 0.0770 chunk 61 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 HIS ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6718 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6367 Z= 0.193 Angle : 0.644 9.666 8643 Z= 0.321 Chirality : 0.042 0.236 966 Planarity : 0.004 0.047 1042 Dihedral : 9.130 87.134 898 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 20.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.22 % Allowed : 31.83 % Favored : 63.95 % 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: -0.48 (0.32), residues: 722 helix: 0.32 (0.28), residues: 363 sheet: -1.81 (0.74), residues: 43 loop : -0.75 (0.38), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 888 HIS 0.002 0.001 HIS A 561 PHE 0.017 0.001 PHE A 291 TYR 0.013 0.001 TYR A 823 ARG 0.006 0.001 ARG A 680 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 160 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 MET cc_start: 0.3712 (mmt) cc_final: 0.3346 (mmt) REVERT: A 285 GLN cc_start: 0.7164 (mp10) cc_final: 0.6919 (mp10) REVERT: A 408 GLN cc_start: 0.8519 (mm110) cc_final: 0.8097 (mt0) REVERT: A 479 GLU cc_start: 0.6846 (tp30) cc_final: 0.6448 (tp30) REVERT: A 505 LEU cc_start: 0.7868 (mp) cc_final: 0.7619 (mp) REVERT: A 536 MET cc_start: 0.6859 (ptp) cc_final: 0.6554 (ptp) REVERT: A 538 ILE cc_start: 0.7734 (mm) cc_final: 0.7503 (mp) REVERT: A 560 HIS cc_start: 0.7503 (t-90) cc_final: 0.6884 (t-90) REVERT: A 578 LYS cc_start: 0.7717 (tttm) cc_final: 0.7342 (tttp) REVERT: A 607 LYS cc_start: 0.7914 (tptt) cc_final: 0.7596 (tppt) REVERT: A 617 LEU cc_start: 0.5495 (OUTLIER) cc_final: 0.5223 (tp) REVERT: A 636 LYS cc_start: 0.8141 (pttp) cc_final: 0.7565 (mtmm) REVERT: A 651 PHE cc_start: 0.7142 (p90) cc_final: 0.6449 (p90) REVERT: A 666 LEU cc_start: 0.8685 (mm) cc_final: 0.8353 (mm) REVERT: A 667 LEU cc_start: 0.8917 (mt) cc_final: 0.8672 (mt) REVERT: A 668 PHE cc_start: 0.8942 (t80) cc_final: 0.8714 (t80) REVERT: A 672 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7949 (mm) REVERT: A 673 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7052 (tm-30) REVERT: A 705 ILE cc_start: 0.7109 (mt) cc_final: 0.6644 (pt) REVERT: A 710 ASN cc_start: 0.7578 (t0) cc_final: 0.7327 (t0) REVERT: A 742 LEU cc_start: 0.8222 (tp) cc_final: 0.7971 (mp) REVERT: A 759 PHE cc_start: 0.7808 (m-80) cc_final: 0.7298 (t80) REVERT: A 793 LYS cc_start: 0.9004 (mttt) cc_final: 0.8448 (mttt) REVERT: A 815 MET cc_start: 0.6143 (tmm) cc_final: 0.5363 (tmm) REVERT: A 834 MET cc_start: 0.7282 (tmm) cc_final: 0.6767 (tmm) REVERT: A 876 LYS cc_start: 0.7880 (tptt) cc_final: 0.7670 (tptt) REVERT: A 890 TRP cc_start: 0.6982 (OUTLIER) cc_final: 0.6583 (m100) REVERT: A 919 LYS cc_start: 0.7934 (tmtt) cc_final: 0.7568 (ttpt) REVERT: A 939 ASN cc_start: 0.7135 (OUTLIER) cc_final: 0.6173 (t0) REVERT: A 1028 ARG cc_start: 0.8266 (mmm-85) cc_final: 0.7995 (tpp80) REVERT: A 1040 PHE cc_start: 0.7614 (m-80) cc_final: 0.7336 (m-80) REVERT: A 1047 LYS cc_start: 0.7799 (tttt) cc_final: 0.7456 (tttp) REVERT: A 1059 GLN cc_start: 0.7153 (pp30) cc_final: 0.6790 (pp30) outliers start: 28 outliers final: 23 residues processed: 175 average time/residue: 0.2086 time to fit residues: 46.3355 Evaluate side-chains 186 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 159 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 288 TRP Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 594 HIS Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain A residue 800 LYS Chi-restraints excluded: chain A residue 810 ILE Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 890 TRP Chi-restraints excluded: chain A residue 898 GLN Chi-restraints excluded: chain A residue 908 MET Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 939 ASN Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 1035 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 53 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 10 optimal weight: 0.0570 chunk 50 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 41 optimal weight: 0.0370 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 HIS ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.159215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.132573 restraints weight = 11349.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.137284 restraints weight = 6549.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.140694 restraints weight = 4336.202| |-----------------------------------------------------------------------------| r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6565 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6367 Z= 0.190 Angle : 0.647 9.698 8643 Z= 0.325 Chirality : 0.042 0.228 966 Planarity : 0.004 0.048 1042 Dihedral : 9.098 86.969 898 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 20.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.52 % Allowed : 31.83 % Favored : 63.65 % 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: -0.51 (0.33), residues: 722 helix: 0.27 (0.28), residues: 363 sheet: -1.81 (0.75), residues: 43 loop : -0.73 (0.38), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 888 HIS 0.005 0.001 HIS A 594 PHE 0.019 0.001 PHE A 291 TYR 0.015 0.001 TYR A 823 ARG 0.006 0.000 ARG A 680 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2003.15 seconds wall clock time: 36 minutes 45.15 seconds (2205.15 seconds total)