Starting phenix.real_space_refine on Fri Mar 15 06:39:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gh6_40033/03_2024/8gh6_40033_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gh6_40033/03_2024/8gh6_40033.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gh6_40033/03_2024/8gh6_40033.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gh6_40033/03_2024/8gh6_40033.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gh6_40033/03_2024/8gh6_40033_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gh6_40033/03_2024/8gh6_40033_updated.pdb" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 121 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 178 5.49 5 Mg 1 5.21 5 S 37 5.16 5 C 6167 2.51 5 N 2043 2.21 5 O 2357 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 118": "OE1" <-> "OE2" Residue "A PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 345": "OE1" <-> "OE2" Residue "A GLU 437": "OE1" <-> "OE2" Residue "A GLU 454": "OE1" <-> "OE2" Residue "A GLU 610": "OE1" <-> "OE2" Residue "A GLU 617": "OE1" <-> "OE2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A GLU 682": "OE1" <-> "OE2" Residue "A ASP 767": "OD1" <-> "OD2" Residue "A ASP 853": "OD1" <-> "OD2" Residue "A GLU 867": "OE1" <-> "OE2" Residue "A ASP 874": "OD1" <-> "OD2" Residue "A GLU 929": "OE1" <-> "OE2" Residue "A ASP 1002": "OD1" <-> "OD2" Residue "A GLU 1035": "OE1" <-> "OE2" Residue "A GLU 1038": "OE1" <-> "OE2" Residue "A GLU 1072": "OE1" <-> "OE2" Residue "A GLU 1081": "OE1" <-> "OE2" Residue "A PHE 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 10785 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 898, 7099 Classifications: {'peptide': 898} Link IDs: {'PTRANS': 43, 'TRANS': 854} Chain breaks: 2 Chain: "B" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 952 Classifications: {'DNA': 47} Link IDs: {'rna3p': 46} Chain: "P" Number of atoms: 493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 493 Classifications: {'DNA': 24} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 23} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 831 Classifications: {'RNA': 39} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 18, 'rna3p_pyr': 14} Link IDs: {'rna2p': 7, 'rna3p': 31} Chain breaks: 2 Chain: "T" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1378 Classifications: {'DNA': 67} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 66} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 32 Unusual residues: {' MG': 1, ' ZN': 2, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 31 SG CYS A 114 33.451 59.687 66.101 1.00 60.08 S ATOM 57 SG CYS A 117 31.222 62.771 66.997 1.00 68.26 S ATOM 5726 SG CYS A 934 15.398 126.086 52.184 1.00 48.69 S ATOM 5752 SG CYS A 938 15.091 129.108 49.930 1.00 52.23 S ATOM 5857 SG CYS A 951 18.013 129.038 52.332 1.00 47.75 S Time building chain proxies: 6.06, per 1000 atoms: 0.56 Number of scatterers: 10785 At special positions: 0 Unit cell: (110.5, 164.424, 107.848, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 37 16.00 P 178 15.00 Mg 1 11.99 O 2357 8.00 N 2043 7.00 C 6167 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.95 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1201 " pdb="ZN ZN A1201 " - pdb=" NE2 HIS A 130 " pdb="ZN ZN A1201 " - pdb=" NE2 HIS A 135 " pdb="ZN ZN A1201 " - pdb=" SG CYS A 117 " pdb="ZN ZN A1201 " - pdb=" SG CYS A 114 " pdb=" ZN A1202 " pdb="ZN ZN A1202 " - pdb=" NE2 HIS A 946 " pdb="ZN ZN A1202 " - pdb=" SG CYS A 938 " pdb="ZN ZN A1202 " - pdb=" SG CYS A 934 " pdb="ZN ZN A1202 " - pdb=" SG CYS A 951 " Number of angles added : 5 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1654 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 6 sheets defined 51.0% alpha, 7.1% beta 74 base pairs and 133 stacking pairs defined. Time for finding SS restraints: 5.30 Creating SS restraints... Processing helix chain 'A' and resid 124 through 134 Processing helix chain 'A' and resid 136 through 142 Processing helix chain 'A' and resid 154 through 170 removed outlier: 3.524A pdb=" N LEU A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 182 removed outlier: 3.826A pdb=" N GLY A 181 " --> pdb=" O GLY A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 197 Processing helix chain 'A' and resid 200 through 213 removed outlier: 3.852A pdb=" N GLN A 207 " --> pdb=" O ARG A 203 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG A 212 " --> pdb=" O ALA A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 323 removed outlier: 3.579A pdb=" N GLU A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS A 322 " --> pdb=" O GLN A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 334 Processing helix chain 'A' and resid 344 through 356 removed outlier: 3.834A pdb=" N TYR A 350 " --> pdb=" O GLU A 346 " (cutoff:3.500A) Proline residue: A 353 - end of helix Processing helix chain 'A' and resid 366 through 372 Processing helix chain 'A' and resid 393 through 398 Processing helix chain 'A' and resid 414 through 418 Processing helix chain 'A' and resid 422 through 435 Processing helix chain 'A' and resid 440 through 443 Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 470 through 486 Processing helix chain 'A' and resid 501 through 519 removed outlier: 3.585A pdb=" N ARG A 517 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 536 No H-bonds generated for 'chain 'A' and resid 534 through 536' Processing helix chain 'A' and resid 539 through 548 Processing helix chain 'A' and resid 553 through 564 Processing helix chain 'A' and resid 593 through 606 removed outlier: 3.613A pdb=" N VAL A 599 " --> pdb=" O ILE A 595 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU A 603 " --> pdb=" O VAL A 599 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE A 604 " --> pdb=" O VAL A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 654 removed outlier: 3.513A pdb=" N MET A 654 " --> pdb=" O VAL A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 729 Processing helix chain 'A' and resid 734 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.705A pdb=" N GLN A 750 " --> pdb=" O ILE A 746 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N HIS A 751 " --> pdb=" O PRO A 747 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLY A 752 " --> pdb=" O ARG A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 777 Processing helix chain 'A' and resid 803 through 820 Proline residue: A 808 - end of helix removed outlier: 4.705A pdb=" N GLY A 817 " --> pdb=" O ARG A 813 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU A 818 " --> pdb=" O ARG A 814 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ASP A 819 " --> pdb=" O PHE A 815 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N SER A 820 " --> pdb=" O GLY A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 830 Processing helix chain 'A' and resid 833 through 848 Processing helix chain 'A' and resid 861 through 871 Processing helix chain 'A' and resid 876 through 881 removed outlier: 4.617A pdb=" N GLU A 880 " --> pdb=" O GLU A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 892 removed outlier: 3.731A pdb=" N THR A 888 " --> pdb=" O PRO A 885 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS A 889 " --> pdb=" O THR A 886 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N TRP A 890 " --> pdb=" O SER A 887 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG A 892 " --> pdb=" O LYS A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 897 No H-bonds generated for 'chain 'A' and resid 895 through 897' Processing helix chain 'A' and resid 900 through 910 Processing helix chain 'A' and resid 929 through 931 No H-bonds generated for 'chain 'A' and resid 929 through 931' Processing helix chain 'A' and resid 944 through 949 Processing helix chain 'A' and resid 952 through 975 removed outlier: 3.626A pdb=" N HIS A 955 " --> pdb=" O HIS A 952 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N GLY A 956 " --> pdb=" O ARG A 953 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 964 " --> pdb=" O ARG A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1031 removed outlier: 3.960A pdb=" N LYS A1029 " --> pdb=" O GLU A1025 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N TYR A1030 " --> pdb=" O LYS A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1044 Processing helix chain 'A' and resid 1049 through 1051 No H-bonds generated for 'chain 'A' and resid 1049 through 1051' Processing helix chain 'A' and resid 1067 through 1075 Processing helix chain 'A' and resid 1081 through 1106 removed outlier: 4.222A pdb=" N ILE A1086 " --> pdb=" O PRO A1082 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL A1087 " --> pdb=" O THR A1083 " (cutoff:3.500A) Proline residue: A1088 - end of helix removed outlier: 4.088A pdb=" N THR A1106 " --> pdb=" O PHE A1102 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 568 through 571 removed outlier: 6.888A pdb=" N CYS A 445 " --> pdb=" O THR A 569 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ALA A 571 " --> pdb=" O CYS A 445 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N THR A 447 " --> pdb=" O ALA A 571 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 664 through 668 Processing sheet with id= C, first strand: chain 'A' and resid 614 through 616 Processing sheet with id= D, first strand: chain 'A' and resid 701 through 703 Processing sheet with id= E, first strand: chain 'A' and resid 986 through 988 removed outlier: 3.551A pdb=" N THR A 988 " --> pdb=" O GLY A 991 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 997 through 1001 305 hydrogen bonds defined for protein. 816 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 186 hydrogen bonds 372 hydrogen bond angles 0 basepair planarities 74 basepair parallelities 133 stacking parallelities Total time for adding SS restraints: 5.03 Time building geometry restraints manager: 5.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2686 1.34 - 1.46: 3430 1.46 - 1.58: 4844 1.58 - 1.70: 353 1.70 - 1.83: 53 Bond restraints: 11366 Sorted by residual: bond pdb=" C3' DG B 30 " pdb=" O3' DG B 30 " ideal model delta sigma weight residual 1.422 1.509 -0.087 3.00e-02 1.11e+03 8.36e+00 bond pdb=" C ILE A 470 " pdb=" N PRO A 471 " ideal model delta sigma weight residual 1.335 1.371 -0.036 1.28e-02 6.10e+03 7.92e+00 bond pdb=" C VAL A1087 " pdb=" N PRO A1088 " ideal model delta sigma weight residual 1.335 1.371 -0.035 1.36e-02 5.41e+03 6.73e+00 bond pdb=" CB PRO A 439 " pdb=" CG PRO A 439 " ideal model delta sigma weight residual 1.492 1.606 -0.114 5.00e-02 4.00e+02 5.24e+00 bond pdb=" CB GLU A1038 " pdb=" CG GLU A1038 " ideal model delta sigma weight residual 1.520 1.584 -0.064 3.00e-02 1.11e+03 4.54e+00 ... (remaining 11361 not shown) Histogram of bond angle deviations from ideal: 97.72 - 105.04: 878 105.04 - 112.36: 5843 112.36 - 119.67: 4236 119.67 - 126.99: 4641 126.99 - 134.30: 542 Bond angle restraints: 16140 Sorted by residual: angle pdb=" CB MET A 640 " pdb=" CG MET A 640 " pdb=" SD MET A 640 " ideal model delta sigma weight residual 112.70 132.09 -19.39 3.00e+00 1.11e-01 4.18e+01 angle pdb=" CA ARG A 171 " pdb=" CB ARG A 171 " pdb=" CG ARG A 171 " ideal model delta sigma weight residual 114.10 126.21 -12.11 2.00e+00 2.50e-01 3.66e+01 angle pdb=" CA GLU A1050 " pdb=" CB GLU A1050 " pdb=" CG GLU A1050 " ideal model delta sigma weight residual 114.10 125.80 -11.70 2.00e+00 2.50e-01 3.42e+01 angle pdb=" CA PRO A 439 " pdb=" N PRO A 439 " pdb=" CD PRO A 439 " ideal model delta sigma weight residual 112.00 104.15 7.85 1.40e+00 5.10e-01 3.15e+01 angle pdb=" C3' A R 245 " pdb=" O3' A R 245 " pdb=" P A R 246 " ideal model delta sigma weight residual 120.20 128.13 -7.93 1.50e+00 4.44e-01 2.79e+01 ... (remaining 16135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.75: 5708 33.75 - 67.50: 770 67.50 - 101.25: 30 101.25 - 135.00: 0 135.00 - 168.75: 5 Dihedral angle restraints: 6513 sinusoidal: 3949 harmonic: 2564 Sorted by residual: dihedral pdb=" C2 TTP A1204 " pdb=" C1' TTP A1204 " pdb=" N1 TTP A1204 " pdb=" O4' TTP A1204 " ideal model delta sinusoidal sigma weight residual 301.68 150.70 150.98 1 2.00e+01 2.50e-03 4.50e+01 dihedral pdb=" O4' A R 245 " pdb=" C1' A R 245 " pdb=" N9 A R 245 " pdb=" C4 A R 245 " ideal model delta sinusoidal sigma weight residual 254.00 175.06 78.94 1 1.70e+01 3.46e-03 2.68e+01 dihedral pdb=" CA PRO A 609 " pdb=" C PRO A 609 " pdb=" N GLU A 610 " pdb=" CA GLU A 610 " ideal model delta harmonic sigma weight residual -180.00 -155.34 -24.66 0 5.00e+00 4.00e-02 2.43e+01 ... (remaining 6510 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1561 0.082 - 0.164: 230 0.164 - 0.246: 19 0.246 - 0.327: 2 0.327 - 0.409: 3 Chirality restraints: 1815 Sorted by residual: chirality pdb=" CB ILE A 911 " pdb=" CA ILE A 911 " pdb=" CG1 ILE A 911 " pdb=" CG2 ILE A 911 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" P DT P 24 " pdb=" OP1 DT P 24 " pdb=" OP2 DT P 24 " pdb=" O5' DT P 24 " both_signs ideal model delta sigma weight residual True 2.35 -2.74 -0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" C3' A R 245 " pdb=" C4' A R 245 " pdb=" O3' A R 245 " pdb=" C2' A R 245 " both_signs ideal model delta sigma weight residual False -2.74 -2.40 -0.34 2.00e-01 2.50e+01 2.92e+00 ... (remaining 1812 not shown) Planarity restraints: 1449 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 438 " 0.079 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO A 439 " -0.197 5.00e-02 4.00e+02 pdb=" CA PRO A 439 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO A 439 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS A1023 " 0.017 2.00e-02 2.50e+03 3.67e-02 2.02e+01 pdb=" CG HIS A1023 " -0.072 2.00e-02 2.50e+03 pdb=" ND1 HIS A1023 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 HIS A1023 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 HIS A1023 " -0.012 2.00e-02 2.50e+03 pdb=" NE2 HIS A1023 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 197 " -0.308 9.50e-02 1.11e+02 1.39e-01 1.45e+01 pdb=" NE ARG A 197 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG A 197 " -0.025 2.00e-02 2.50e+03 pdb=" NH1 ARG A 197 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG A 197 " -0.002 2.00e-02 2.50e+03 ... (remaining 1446 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 305 2.68 - 3.24: 8637 3.24 - 3.79: 18795 3.79 - 4.35: 25075 4.35 - 4.90: 36701 Nonbonded interactions: 89513 Sorted by model distance: nonbonded pdb=" O PHE A 530 " pdb="MG MG A1203 " model vdw 2.128 2.170 nonbonded pdb=" OD2 ASP A 628 " pdb="MG MG A1203 " model vdw 2.159 2.170 nonbonded pdb="MG MG A1203 " pdb=" O1A TTP A1204 " model vdw 2.213 2.170 nonbonded pdb=" O LYS A 131 " pdb=" OG1 THR A 139 " model vdw 2.332 2.440 nonbonded pdb=" O ILE A 497 " pdb=" O2' A R 250 " model vdw 2.346 2.440 ... (remaining 89508 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.020 Extract box with map and model: 6.390 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 37.100 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 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 : 0.006 0.114 11366 Z= 0.364 Angle : 1.101 19.394 16140 Z= 0.600 Chirality : 0.058 0.409 1815 Planarity : 0.010 0.139 1449 Dihedral : 23.181 168.754 4859 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.02 % Favored : 97.87 % Rotamer: Outliers : 0.13 % Allowed : 11.42 % Favored : 88.45 % 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: -1.06 (0.25), residues: 892 helix: -0.88 (0.20), residues: 461 sheet: -0.10 (0.59), residues: 81 loop : -0.31 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A1061 HIS 0.052 0.004 HIS A1023 PHE 0.047 0.004 PHE A 180 TYR 0.054 0.004 TYR A 202 ARG 0.029 0.002 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 0.929 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 104 average time/residue: 0.4001 time to fit residues: 52.1833 Evaluate side-chains 76 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.4980 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 653 GLN A 678 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11366 Z= 0.194 Angle : 0.598 8.719 16140 Z= 0.342 Chirality : 0.040 0.267 1815 Planarity : 0.005 0.054 1449 Dihedral : 25.594 165.255 3117 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.02 % Favored : 97.87 % Rotamer: Outliers : 2.66 % Allowed : 8.23 % Favored : 89.11 % 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: 0.15 (0.27), residues: 892 helix: 0.44 (0.23), residues: 462 sheet: -0.03 (0.54), residues: 93 loop : -0.12 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1061 HIS 0.010 0.001 HIS A1096 PHE 0.013 0.001 PHE A 968 TYR 0.014 0.002 TYR A 788 ARG 0.008 0.001 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 84 time to evaluate : 1.136 Fit side-chains REVERT: A 369 LEU cc_start: 0.7011 (mt) cc_final: 0.6784 (mm) REVERT: A 540 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6623 (tt0) REVERT: A 1080 ARG cc_start: 0.6878 (mtp85) cc_final: 0.6346 (tpt90) outliers start: 20 outliers final: 8 residues processed: 94 average time/residue: 0.3331 time to fit residues: 41.3290 Evaluate side-chains 83 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 686 ASN Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 979 THR Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1055 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 0.7980 chunk 29 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 93 optimal weight: 20.0000 chunk 32 optimal weight: 10.0000 chunk 75 optimal weight: 0.6980 overall best weight: 5.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 751 HIS A 870 HIS A 910 HIS A 952 HIS A1096 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 11366 Z= 0.519 Angle : 0.807 9.445 16140 Z= 0.443 Chirality : 0.050 0.277 1815 Planarity : 0.007 0.052 1449 Dihedral : 26.412 165.398 3117 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.14 % Favored : 96.75 % Rotamer: Outliers : 2.79 % Allowed : 11.69 % Favored : 85.52 % 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: -0.60 (0.27), residues: 892 helix: -0.12 (0.23), residues: 463 sheet: 0.49 (0.62), residues: 66 loop : -0.78 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A1061 HIS 0.013 0.003 HIS A 910 PHE 0.024 0.003 PHE A 749 TYR 0.026 0.003 TYR A 788 ARG 0.009 0.001 ARG A 171 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 68 time to evaluate : 0.921 Fit side-chains REVERT: A 369 LEU cc_start: 0.7067 (mt) cc_final: 0.6770 (mm) REVERT: A 1071 LYS cc_start: 0.8232 (mmtt) cc_final: 0.7900 (mtmt) outliers start: 21 outliers final: 12 residues processed: 81 average time/residue: 0.3131 time to fit residues: 33.7983 Evaluate side-chains 73 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 61 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 979 THR Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1004 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 20.0000 chunk 71 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11366 Z= 0.179 Angle : 0.571 9.592 16140 Z= 0.325 Chirality : 0.038 0.265 1815 Planarity : 0.004 0.047 1449 Dihedral : 25.915 166.886 3117 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.68 % Favored : 98.21 % Rotamer: Outliers : 1.86 % Allowed : 12.22 % Favored : 85.92 % 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: 0.31 (0.28), residues: 892 helix: 0.75 (0.24), residues: 461 sheet: 0.69 (0.72), residues: 54 loop : -0.44 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 701 HIS 0.006 0.001 HIS A1096 PHE 0.011 0.001 PHE A 968 TYR 0.010 0.001 TYR A 202 ARG 0.005 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 1.004 Fit side-chains REVERT: A 369 LEU cc_start: 0.7028 (mt) cc_final: 0.6794 (mm) REVERT: A 510 ASP cc_start: 0.8690 (t0) cc_final: 0.8403 (t70) REVERT: A 687 ILE cc_start: 0.8742 (mt) cc_final: 0.8510 (mt) REVERT: A 1046 LEU cc_start: 0.5400 (OUTLIER) cc_final: 0.5014 (pp) outliers start: 14 outliers final: 10 residues processed: 84 average time/residue: 0.2995 time to fit residues: 33.6715 Evaluate side-chains 81 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 70 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 686 ASN Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1046 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11366 Z= 0.233 Angle : 0.593 9.868 16140 Z= 0.332 Chirality : 0.039 0.245 1815 Planarity : 0.005 0.046 1449 Dihedral : 26.012 168.939 3117 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.47 % Favored : 97.42 % Rotamer: Outliers : 3.45 % Allowed : 11.16 % Favored : 85.39 % 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: 0.36 (0.28), residues: 892 helix: 0.81 (0.24), residues: 466 sheet: 0.64 (0.71), residues: 54 loop : -0.46 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1061 HIS 0.006 0.001 HIS A1096 PHE 0.012 0.001 PHE A 749 TYR 0.015 0.002 TYR A 202 ARG 0.005 0.000 ARG A 611 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 70 time to evaluate : 0.886 Fit side-chains REVERT: A 190 LEU cc_start: 0.6893 (OUTLIER) cc_final: 0.6670 (tt) REVERT: A 369 LEU cc_start: 0.7033 (mt) cc_final: 0.6769 (mm) REVERT: A 510 ASP cc_start: 0.8700 (t0) cc_final: 0.8474 (t70) REVERT: A 617 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.6270 (mp0) REVERT: A 687 ILE cc_start: 0.8714 (mt) cc_final: 0.8513 (mt) REVERT: A 767 ASP cc_start: 0.8396 (m-30) cc_final: 0.7912 (m-30) REVERT: A 1046 LEU cc_start: 0.5439 (OUTLIER) cc_final: 0.5026 (pp) outliers start: 26 outliers final: 20 residues processed: 89 average time/residue: 0.2854 time to fit residues: 34.4258 Evaluate side-chains 90 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 67 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 617 GLU Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 686 ASN Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 918 ILE Chi-restraints excluded: chain A residue 979 THR Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1046 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 59 optimal weight: 0.6980 chunk 24 optimal weight: 0.0570 chunk 100 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 97 optimal weight: 20.0000 overall best weight: 1.5502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11366 Z= 0.208 Angle : 0.568 9.988 16140 Z= 0.319 Chirality : 0.038 0.226 1815 Planarity : 0.005 0.044 1449 Dihedral : 25.940 170.287 3117 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.91 % Favored : 97.98 % Rotamer: Outliers : 3.32 % Allowed : 11.69 % Favored : 84.99 % 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: 0.56 (0.28), residues: 892 helix: 1.02 (0.24), residues: 466 sheet: 0.66 (0.71), residues: 54 loop : -0.42 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1061 HIS 0.006 0.001 HIS A1096 PHE 0.010 0.001 PHE A 749 TYR 0.013 0.002 TYR A 202 ARG 0.007 0.000 ARG A 611 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 70 time to evaluate : 0.890 Fit side-chains REVERT: A 369 LEU cc_start: 0.7038 (mt) cc_final: 0.6806 (mm) REVERT: A 510 ASP cc_start: 0.8669 (t0) cc_final: 0.8406 (t70) REVERT: A 617 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.6207 (mp0) REVERT: A 767 ASP cc_start: 0.8411 (m-30) cc_final: 0.7911 (m-30) REVERT: A 1046 LEU cc_start: 0.5407 (OUTLIER) cc_final: 0.4989 (pp) outliers start: 25 outliers final: 20 residues processed: 88 average time/residue: 0.2951 time to fit residues: 34.9643 Evaluate side-chains 89 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 67 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 617 GLU Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 686 ASN Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 918 ILE Chi-restraints excluded: chain A residue 979 THR Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1046 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 6.9990 chunk 57 optimal weight: 0.1980 chunk 73 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 84 optimal weight: 8.9990 chunk 100 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11366 Z= 0.194 Angle : 0.558 10.203 16140 Z= 0.311 Chirality : 0.038 0.207 1815 Planarity : 0.005 0.044 1449 Dihedral : 25.850 173.010 3117 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.47 % Favored : 97.42 % Rotamer: Outliers : 2.66 % Allowed : 12.48 % Favored : 84.86 % 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: 0.62 (0.29), residues: 892 helix: 1.04 (0.24), residues: 477 sheet: 0.63 (0.71), residues: 54 loop : -0.37 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1061 HIS 0.005 0.001 HIS A1096 PHE 0.009 0.001 PHE A 749 TYR 0.012 0.001 TYR A 202 ARG 0.006 0.000 ARG A 764 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 70 time to evaluate : 1.038 Fit side-chains REVERT: A 369 LEU cc_start: 0.7055 (mt) cc_final: 0.6826 (mm) REVERT: A 510 ASP cc_start: 0.8623 (t0) cc_final: 0.8397 (t70) REVERT: A 617 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.6244 (mp0) REVERT: A 767 ASP cc_start: 0.8411 (m-30) cc_final: 0.7901 (m-30) REVERT: A 1046 LEU cc_start: 0.5447 (OUTLIER) cc_final: 0.5023 (pp) outliers start: 20 outliers final: 16 residues processed: 87 average time/residue: 0.2923 time to fit residues: 34.2566 Evaluate side-chains 82 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 64 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 617 GLU Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 686 ASN Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 918 ILE Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1046 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 63 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 49 optimal weight: 0.0270 chunk 9 optimal weight: 0.8980 chunk 78 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 93 optimal weight: 20.0000 overall best weight: 1.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11366 Z= 0.196 Angle : 0.551 10.230 16140 Z= 0.309 Chirality : 0.037 0.208 1815 Planarity : 0.004 0.044 1449 Dihedral : 25.788 175.728 3117 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.35 % Favored : 97.53 % Rotamer: Outliers : 2.79 % Allowed : 12.22 % Favored : 84.99 % 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: 0.68 (0.29), residues: 892 helix: 1.13 (0.24), residues: 473 sheet: 0.66 (0.72), residues: 54 loop : -0.39 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1061 HIS 0.006 0.001 HIS A 955 PHE 0.009 0.001 PHE A 749 TYR 0.013 0.001 TYR A 350 ARG 0.009 0.000 ARG A 611 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 67 time to evaluate : 0.923 Fit side-chains REVERT: A 369 LEU cc_start: 0.7051 (mt) cc_final: 0.6829 (mm) REVERT: A 510 ASP cc_start: 0.8646 (t0) cc_final: 0.8421 (t70) REVERT: A 617 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.6227 (mp0) REVERT: A 767 ASP cc_start: 0.8416 (m-30) cc_final: 0.7902 (m-30) REVERT: A 1046 LEU cc_start: 0.5482 (OUTLIER) cc_final: 0.5056 (pp) outliers start: 21 outliers final: 19 residues processed: 84 average time/residue: 0.2937 time to fit residues: 33.3360 Evaluate side-chains 86 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 65 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 617 GLU Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 686 ASN Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 918 ILE Chi-restraints excluded: chain A residue 979 THR Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1046 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 10.0000 chunk 56 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 84 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 93 optimal weight: 20.0000 chunk 61 optimal weight: 3.9990 chunk 98 optimal weight: 20.0000 chunk 60 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 744 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11366 Z= 0.157 Angle : 0.523 9.900 16140 Z= 0.294 Chirality : 0.036 0.209 1815 Planarity : 0.004 0.045 1449 Dihedral : 25.659 177.117 3117 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.91 % Favored : 97.98 % Rotamer: Outliers : 2.39 % Allowed : 12.88 % Favored : 84.73 % 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: 0.99 (0.29), residues: 892 helix: 1.32 (0.25), residues: 478 sheet: 0.69 (0.63), residues: 71 loop : -0.18 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 701 HIS 0.006 0.001 HIS A 955 PHE 0.008 0.001 PHE A 968 TYR 0.007 0.001 TYR A 788 ARG 0.008 0.000 ARG A 418 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 74 time to evaluate : 0.823 Fit side-chains REVERT: A 369 LEU cc_start: 0.7044 (mt) cc_final: 0.6838 (mm) REVERT: A 617 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.6191 (mp0) REVERT: A 767 ASP cc_start: 0.8403 (m-30) cc_final: 0.7830 (m-30) REVERT: A 1046 LEU cc_start: 0.5516 (OUTLIER) cc_final: 0.5093 (pp) outliers start: 18 outliers final: 10 residues processed: 88 average time/residue: 0.3102 time to fit residues: 35.8550 Evaluate side-chains 81 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 69 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 617 GLU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 686 ASN Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 979 THR Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1046 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 82 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 87 optimal weight: 0.0370 chunk 25 optimal weight: 5.9990 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1033 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11366 Z= 0.165 Angle : 0.529 8.357 16140 Z= 0.298 Chirality : 0.036 0.186 1815 Planarity : 0.004 0.044 1449 Dihedral : 25.630 178.071 3117 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.02 % Favored : 97.87 % Rotamer: Outliers : 1.73 % Allowed : 13.28 % Favored : 84.99 % 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: 0.94 (0.29), residues: 892 helix: 1.31 (0.25), residues: 474 sheet: 0.62 (0.62), residues: 71 loop : -0.24 (0.35), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1061 HIS 0.006 0.001 HIS A 955 PHE 0.008 0.001 PHE A 968 TYR 0.014 0.001 TYR A 350 ARG 0.007 0.000 ARG A1053 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 73 time to evaluate : 0.970 Fit side-chains REVERT: A 510 ASP cc_start: 0.8528 (t0) cc_final: 0.8275 (t70) REVERT: A 617 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.6157 (mp0) REVERT: A 1046 LEU cc_start: 0.5478 (OUTLIER) cc_final: 0.5053 (pp) outliers start: 13 outliers final: 11 residues processed: 83 average time/residue: 0.3180 time to fit residues: 35.0710 Evaluate side-chains 81 residues out of total 753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 68 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 617 GLU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 686 ASN Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 979 THR Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1046 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 0.0020 chunk 12 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1033 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.177163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.130168 restraints weight = 14311.140| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.47 r_work: 0.3308 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11366 Z= 0.209 Angle : 0.558 6.227 16140 Z= 0.313 Chirality : 0.037 0.153 1815 Planarity : 0.005 0.067 1449 Dihedral : 25.677 178.035 3117 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.47 % Favored : 97.42 % Rotamer: Outliers : 2.12 % Allowed : 13.01 % Favored : 84.86 % 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: 0.73 (0.29), residues: 892 helix: 1.18 (0.24), residues: 472 sheet: -0.02 (0.64), residues: 66 loop : -0.26 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1061 HIS 0.006 0.001 HIS A 955 PHE 0.010 0.001 PHE A 749 TYR 0.013 0.001 TYR A 788 ARG 0.006 0.000 ARG A 418 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2109.83 seconds wall clock time: 38 minutes 39.81 seconds (2319.81 seconds total)