Starting phenix.real_space_refine on Fri Sep 11 17:26:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mc5_63789/09_2026/9mc5_63789_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mc5_63789/09_2026/9mc5_63789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mc5_63789/09_2026/9mc5_63789_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mc5_63789/09_2026/9mc5_63789_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mc5_63789/09_2026/9mc5_63789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mc5_63789/09_2026/9mc5_63789.map" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.010 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 1 5.49 5 S 49 5.16 5 C 6499 2.51 5 N 1748 2.21 5 O 1920 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10217 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 957, 7539 Classifications: {'peptide': 957} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 49, 'TRANS': 907} Chain breaks: 2 Chain: "B" Number of atoms: 2047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2047 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 16, 'TRANS': 237} Chain breaks: 2 Chain: "C" Number of atoms: 608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 608 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 2.18, per 1000 atoms: 0.21 Number of scatterers: 10217 At special positions: 0 Unit cell: (93.312, 108.216, 125.712, 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 49 16.00 P 1 15.00 O 1920 8.00 N 1748 7.00 C 6499 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 - 3.00 Amino acid : True - 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: 0.84 Conformation dependent library (CDL) restraints added in 347.3 milliseconds 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2408 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 9 sheets defined 47.4% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 82 through 95 Processing helix chain 'A' and resid 108 through 114 removed outlier: 3.640A pdb=" N SER A 113 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 123 removed outlier: 4.048A pdb=" N ILE A 123 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 137 Proline residue: A 133 - end of helix removed outlier: 3.920A pdb=" N GLU A 137 " --> pdb=" O PRO A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 158 removed outlier: 3.910A pdb=" N GLY A 158 " --> pdb=" O ASP A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 183 Processing helix chain 'A' and resid 256 through 260 Processing helix chain 'A' and resid 305 through 312 Processing helix chain 'A' and resid 319 through 323 removed outlier: 3.765A pdb=" N PHE A 323 " --> pdb=" O PHE A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 344 removed outlier: 3.976A pdb=" N GLN A 328 " --> pdb=" O SER A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 369 Processing helix chain 'A' and resid 379 through 389 Processing helix chain 'A' and resid 394 through 415 Processing helix chain 'A' and resid 429 through 432 Processing helix chain 'A' and resid 435 through 439 removed outlier: 3.774A pdb=" N LEU A 439 " --> pdb=" O LYS A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 459 removed outlier: 4.393A pdb=" N VAL A 457 " --> pdb=" O GLY A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 469 Processing helix chain 'A' and resid 477 through 491 Processing helix chain 'A' and resid 512 through 516 Processing helix chain 'A' and resid 520 through 524 removed outlier: 3.586A pdb=" N VAL A 524 " --> pdb=" O PRO A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 540 Processing helix chain 'A' and resid 553 through 557 removed outlier: 3.749A pdb=" N GLU A 557 " --> pdb=" O PRO A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 567 Processing helix chain 'A' and resid 577 through 592 Processing helix chain 'A' and resid 617 through 621 removed outlier: 3.608A pdb=" N SER A 621 " --> pdb=" O TYR A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 669 Proline residue: A 659 - end of helix Processing helix chain 'A' and resid 671 through 679 Processing helix chain 'A' and resid 682 through 698 Processing helix chain 'A' and resid 702 through 718 Processing helix chain 'A' and resid 718 through 728 Processing helix chain 'A' and resid 758 through 776 removed outlier: 3.574A pdb=" N LEU A 762 " --> pdb=" O ASN A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 792 removed outlier: 3.768A pdb=" N VAL A 787 " --> pdb=" O ASP A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 833 Processing helix chain 'A' and resid 835 through 839 Processing helix chain 'A' and resid 857 through 873 Processing helix chain 'A' and resid 879 through 888 Processing helix chain 'A' and resid 894 through 915 removed outlier: 3.539A pdb=" N THR A 898 " --> pdb=" O ILE A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 982 Processing helix chain 'A' and resid 1003 through 1011 Processing helix chain 'A' and resid 1014 through 1024 Processing helix chain 'B' and resid 950 through 969 Processing helix chain 'B' and resid 1050 through 1054 Processing helix chain 'B' and resid 1060 through 1073 removed outlier: 3.936A pdb=" N ILE B1072 " --> pdb=" O ILE B1068 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1081 removed outlier: 4.091A pdb=" N TYR B1079 " --> pdb=" O GLU B1076 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLU B1081 " --> pdb=" O TYR B1078 " (cutoff:3.500A) Processing helix chain 'B' and resid 1090 through 1118 Processing helix chain 'B' and resid 1123 through 1131 Processing helix chain 'B' and resid 1132 through 1151 Processing helix chain 'B' and resid 1265 through 1284 removed outlier: 4.130A pdb=" N THR B1274 " --> pdb=" O ARG B1270 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N GLN B1275 " --> pdb=" O GLY B1271 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N PHE B1276 " --> pdb=" O VAL B1272 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B1280 " --> pdb=" O PHE B1276 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU B1281 " --> pdb=" O ARG B1277 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA B1283 " --> pdb=" O ALA B1279 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY B1284 " --> pdb=" O LEU B1280 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 35 Processing helix chain 'C' and resid 37 through 41 Processing helix chain 'C' and resid 55 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 144 through 147 removed outlier: 6.708A pdb=" N VAL A 99 " --> pdb=" O THR A 145 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N TYR A 147 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU A 101 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL A 75 " --> pdb=" O THR A 100 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N HIS A 102 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL A 77 " --> pdb=" O HIS A 102 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL A 316 " --> pdb=" O TYR A 425 " (cutoff:3.500A) removed outlier: 9.456A pdb=" N ASP A 427 " --> pdb=" O VAL A 316 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 206 through 208 Processing sheet with id=AA3, first strand: chain 'A' and resid 265 through 266 removed outlier: 6.790A pdb=" N THR A 233 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS A 268 " --> pdb=" O SER A 276 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 545 through 548 removed outlier: 6.084A pdb=" N ILE A 500 " --> pdb=" O THR A 546 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N HIS A 548 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL A 502 " --> pdb=" O HIS A 548 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N TYR A 471 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N THR A 503 " --> pdb=" O TYR A 471 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU A 473 " --> pdb=" O THR A 503 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS A 470 " --> pdb=" O GLY A 570 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ALA A 572 " --> pdb=" O LYS A 470 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N PHE A 472 " --> pdb=" O ALA A 572 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL A 571 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N SER A 598 " --> pdb=" O VAL A 571 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ASN A 573 " --> pdb=" O SER A 598 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N THR A 600 " --> pdb=" O ASN A 573 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 945 through 947 Processing sheet with id=AA6, first strand: chain 'A' and resid 958 through 961 removed outlier: 6.857A pdb=" N PHE A 958 " --> pdb=" O ARG A1054 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N THR A1056 " --> pdb=" O PHE A 958 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL A 960 " --> pdb=" O THR A1056 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ASN A1041 " --> pdb=" O ILE A 987 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ILE A 987 " --> pdb=" O ASN A1041 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLN A 992 " --> pdb=" O MET A 996 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N MET A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 958 through 961 removed outlier: 6.857A pdb=" N PHE A 958 " --> pdb=" O ARG A1054 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N THR A1056 " --> pdb=" O PHE A 958 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL A 960 " --> pdb=" O THR A1056 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N CYS A1040 " --> pdb=" O VAL A1048 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 929 through 932 removed outlier: 3.957A pdb=" N PHE B 978 " --> pdb=" O LEU B 984 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N LEU B 984 " --> pdb=" O PHE B 978 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 12 through 17 removed outlier: 3.881A pdb=" N ARG C 42 " --> pdb=" O VAL C 70 " (cutoff:3.500A) 495 hydrogen bonds defined for protein. 1356 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.72 Time building geometry restraints manager: 1.07 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: 3368 1.34 - 1.46: 1632 1.46 - 1.58: 5362 1.58 - 1.70: 1 1.70 - 1.81: 77 Bond restraints: 10440 Sorted by residual: bond pdb=" CA ASN B1030 " pdb=" C ASN B1030 " ideal model delta sigma weight residual 1.517 1.529 -0.013 1.02e-02 9.61e+03 1.51e+00 bond pdb=" C4 AMP A1101 " pdb=" C5 AMP A1101 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.24e+00 bond pdb=" CA ILE B1011 " pdb=" CB ILE B1011 " ideal model delta sigma weight residual 1.532 1.544 -0.011 1.08e-02 8.57e+03 1.12e+00 bond pdb=" CB PRO B1260 " pdb=" CG PRO B1260 " ideal model delta sigma weight residual 1.492 1.544 -0.052 5.00e-02 4.00e+02 1.10e+00 bond pdb=" CB GLN B1114 " pdb=" CG GLN B1114 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.06e+00 ... (remaining 10435 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 13874 2.09 - 4.17: 221 4.17 - 6.26: 43 6.26 - 8.35: 9 8.35 - 10.43: 3 Bond angle restraints: 14150 Sorted by residual: angle pdb=" C HIS B1130 " pdb=" N PHE B1131 " pdb=" CA PHE B1131 " ideal model delta sigma weight residual 121.52 113.25 8.27 2.34e+00 1.83e-01 1.25e+01 angle pdb=" C ASN B1030 " pdb=" CA ASN B1030 " pdb=" CB ASN B1030 " ideal model delta sigma weight residual 109.56 114.85 -5.29 1.51e+00 4.39e-01 1.23e+01 angle pdb=" CB MET A 220 " pdb=" CG MET A 220 " pdb=" SD MET A 220 " ideal model delta sigma weight residual 112.70 122.77 -10.07 3.00e+00 1.11e-01 1.13e+01 angle pdb=" CA GLN B1114 " pdb=" CB GLN B1114 " pdb=" CG GLN B1114 " ideal model delta sigma weight residual 114.10 120.67 -6.57 2.00e+00 2.50e-01 1.08e+01 angle pdb=" C GLN A 717 " pdb=" N TYR A 718 " pdb=" CA TYR A 718 " ideal model delta sigma weight residual 122.42 117.35 5.07 1.55e+00 4.16e-01 1.07e+01 ... (remaining 14145 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.61: 5618 16.61 - 33.21: 506 33.21 - 49.82: 117 49.82 - 66.42: 34 66.42 - 83.03: 19 Dihedral angle restraints: 6294 sinusoidal: 2567 harmonic: 3727 Sorted by residual: dihedral pdb=" CA PHE B1256 " pdb=" C PHE B1256 " pdb=" N PRO B1257 " pdb=" CA PRO B1257 " ideal model delta harmonic sigma weight residual 180.00 -156.90 -23.10 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA MET A 421 " pdb=" C MET A 421 " pdb=" N GLN A 422 " pdb=" CA GLN A 422 " ideal model delta harmonic sigma weight residual 180.00 159.03 20.97 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA PHE B1131 " pdb=" C PHE B1131 " pdb=" N SER B1132 " pdb=" CA SER B1132 " ideal model delta harmonic sigma weight residual 180.00 160.39 19.61 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 6291 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 994 0.037 - 0.073: 407 0.073 - 0.110: 136 0.110 - 0.147: 29 0.147 - 0.183: 2 Chirality restraints: 1568 Sorted by residual: chirality pdb=" CA MET A 582 " pdb=" N MET A 582 " pdb=" C MET A 582 " pdb=" CB MET A 582 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.40e-01 chirality pdb=" CA ILE A 875 " pdb=" N ILE A 875 " pdb=" C ILE A 875 " pdb=" CB ILE A 875 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CA VAL B1039 " pdb=" N VAL B1039 " pdb=" C VAL B1039 " pdb=" CB VAL B1039 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.34e-01 ... (remaining 1565 not shown) Planarity restraints: 1849 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 714 " -0.016 2.00e-02 2.50e+03 1.39e-02 4.84e+00 pdb=" CG TRP A 714 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP A 714 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 714 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 714 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 714 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 714 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 714 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 714 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 714 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 709 " 0.009 2.00e-02 2.50e+03 1.34e-02 4.50e+00 pdb=" CG TRP A 709 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP A 709 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP A 709 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 709 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 709 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 709 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 709 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 709 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 709 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 683 " -0.034 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO A 684 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 684 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 684 " -0.029 5.00e-02 4.00e+02 ... (remaining 1846 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 5067 2.98 - 3.46: 10437 3.46 - 3.94: 16836 3.94 - 4.42: 19782 4.42 - 4.90: 31800 Nonbonded interactions: 83922 Sorted by model distance: nonbonded pdb=" O GLN B1114 " pdb=" OE1 GLN B1114 " model vdw 2.504 3.040 nonbonded pdb=" O ASP A 576 " pdb=" OD1 ASP A 576 " model vdw 2.537 3.040 nonbonded pdb=" O TRP B1136 " pdb=" OD1 ASN B1140 " model vdw 2.550 3.040 nonbonded pdb=" N ASN B1030 " pdb=" O ASN B1030 " model vdw 2.574 2.496 nonbonded pdb=" O LEU A 394 " pdb=" OD1 ASN A 398 " model vdw 2.584 3.040 ... (remaining 83917 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 6.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 9.920 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 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 0.052 10440 Z= 0.141 Angle : 0.696 10.432 14150 Z= 0.357 Chirality : 0.044 0.183 1568 Planarity : 0.005 0.052 1849 Dihedral : 14.743 83.029 3886 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.63 % Allowed : 13.08 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.23), residues: 1274 helix: 0.82 (0.22), residues: 517 sheet: -0.02 (0.38), residues: 177 loop : -0.01 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1010 TYR 0.021 0.002 TYR A 910 PHE 0.013 0.001 PHE A 472 TRP 0.038 0.003 TRP A 714 HIS 0.008 0.001 HIS A 715 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (10440) covalent geometry : angle 0.69558 / 0.36 (14150) hydrogen bonds : bond 0.13025 / 8.87 ( 491) hydrogen bonds : angle 6.42518 / 4.54 ( 1356) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 122 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 256 MET cc_start: 0.6972 (mtp) cc_final: 0.6652 (mmt) REVERT: A 761 HIS cc_start: 0.7757 (p-80) cc_final: 0.7360 (p-80) REVERT: B 1058 LYS cc_start: 0.8869 (pttm) cc_final: 0.8343 (mmmt) REVERT: B 1142 ILE cc_start: 0.8483 (mm) cc_final: 0.8259 (pt) REVERT: C 62 GLN cc_start: 0.8041 (mt0) cc_final: 0.7802 (mt0) outliers start: 7 outliers final: 4 residues processed: 125 average time/residue: 0.1037 time to fit residues: 18.1960 Evaluate side-chains 114 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 110 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain B residue 1063 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.0020 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 GLN A 658 GLN A 662 ASN A 867 ASN B1110 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.209920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.164155 restraints weight = 13476.625| |-----------------------------------------------------------------------------| r_work (start): 0.4218 rms_B_bonded: 3.39 r_work: 0.3702 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.0776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10440 Z= 0.142 Angle : 0.606 9.810 14150 Z= 0.306 Chirality : 0.043 0.163 1568 Planarity : 0.005 0.045 1849 Dihedral : 6.310 74.796 1405 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.88 % Allowed : 11.74 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.24), residues: 1274 helix: 1.08 (0.22), residues: 529 sheet: 0.18 (0.38), residues: 191 loop : 0.01 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 586 TYR 0.017 0.001 TYR B1094 PHE 0.013 0.001 PHE A 116 TRP 0.023 0.002 TRP A 714 HIS 0.008 0.001 HIS B1130 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (10440) covalent geometry : angle 0.60578 / 0.31 (14150) hydrogen bonds : bond 0.04019 / 2.61 ( 491) hydrogen bonds : angle 4.97434 / 3.51 ( 1356) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7400 (mt0) REVERT: A 761 HIS cc_start: 0.7567 (p-80) cc_final: 0.7341 (p-80) REVERT: A 844 MET cc_start: 0.7909 (tpp) cc_final: 0.7690 (tpp) REVERT: B 1114 GLN cc_start: 0.8404 (tp-100) cc_final: 0.8183 (tp-100) REVERT: B 1142 ILE cc_start: 0.8636 (mm) cc_final: 0.8364 (pt) outliers start: 21 outliers final: 12 residues processed: 133 average time/residue: 0.1110 time to fit residues: 20.5127 Evaluate side-chains 121 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain B residue 1133 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 32 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 117 optimal weight: 0.0070 chunk 78 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 GLN ** B1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1080 ASN ** B1149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.203669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.138825 restraints weight = 13672.333| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 2.27 r_work: 0.3809 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3642 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10440 Z= 0.124 Angle : 0.561 9.205 14150 Z= 0.281 Chirality : 0.042 0.155 1568 Planarity : 0.004 0.042 1849 Dihedral : 5.734 74.685 1398 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.15 % Allowed : 12.72 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.24), residues: 1274 helix: 1.30 (0.22), residues: 530 sheet: 0.17 (0.38), residues: 196 loop : 0.06 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1029 TYR 0.014 0.001 TYR B1100 PHE 0.014 0.001 PHE A 116 TRP 0.015 0.001 TRP A 423 HIS 0.005 0.001 HIS A 713 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (10440) covalent geometry : angle 0.56069 / 0.28 (14150) hydrogen bonds : bond 0.03693 / 2.40 ( 491) hydrogen bonds : angle 4.60515 / 3.24 ( 1356) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 709 TRP cc_start: 0.8689 (t-100) cc_final: 0.8089 (t60) REVERT: A 761 HIS cc_start: 0.7483 (p-80) cc_final: 0.7249 (p-80) REVERT: A 844 MET cc_start: 0.8040 (tpp) cc_final: 0.7823 (tpp) REVERT: B 942 LYS cc_start: 0.9172 (ttmm) cc_final: 0.8827 (ttmm) REVERT: B 1142 ILE cc_start: 0.8604 (mm) cc_final: 0.8316 (pt) outliers start: 24 outliers final: 15 residues processed: 134 average time/residue: 0.1082 time to fit residues: 20.3420 Evaluate side-chains 128 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain A residue 727 HIS Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain B residue 1133 THR Chi-restraints excluded: chain C residue 67 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 116 optimal weight: 10.0000 chunk 39 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 110 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 GLN A 573 ASN ** B1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.203818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.158501 restraints weight = 13558.632| |-----------------------------------------------------------------------------| r_work (start): 0.4145 rms_B_bonded: 3.55 r_work: 0.3582 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 10440 Z= 0.261 Angle : 0.658 9.267 14150 Z= 0.331 Chirality : 0.045 0.219 1568 Planarity : 0.005 0.046 1849 Dihedral : 6.010 80.540 1398 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.96 % Allowed : 12.81 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.24), residues: 1274 helix: 1.05 (0.22), residues: 531 sheet: -0.20 (0.37), residues: 197 loop : -0.21 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 586 TYR 0.019 0.002 TYR B1094 PHE 0.024 0.002 PHE A 116 TRP 0.014 0.002 TRP A 423 HIS 0.009 0.002 HIS A 715 Details of bonding type rmsd/Z covalent geometry : bond 0.00637 / 0.26 (10440) covalent geometry : angle 0.65795 / 0.33 (14150) hydrogen bonds : bond 0.04334 / 2.79 ( 491) hydrogen bonds : angle 4.80397 / 3.39 ( 1356) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 117 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: A 422 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7989 (mt0) REVERT: A 582 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8222 (mtm) REVERT: A 647 TRP cc_start: 0.9238 (t60) cc_final: 0.8607 (t60) REVERT: A 709 TRP cc_start: 0.8534 (t-100) cc_final: 0.8030 (t60) REVERT: A 761 HIS cc_start: 0.7360 (p-80) cc_final: 0.7141 (p-80) REVERT: B 1022 LEU cc_start: 0.7720 (mt) cc_final: 0.7147 (tt) REVERT: B 1030 ASN cc_start: 0.5673 (p0) cc_final: 0.5436 (p0) REVERT: B 1131 PHE cc_start: 0.8016 (OUTLIER) cc_final: 0.6788 (m-10) REVERT: B 1142 ILE cc_start: 0.8526 (mm) cc_final: 0.8267 (pt) outliers start: 33 outliers final: 17 residues processed: 140 average time/residue: 0.1111 time to fit residues: 21.1209 Evaluate side-chains 129 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 582 MET Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain A residue 727 HIS Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain B residue 1131 PHE Chi-restraints excluded: chain B residue 1133 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 19 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 107 optimal weight: 7.9990 chunk 120 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 64 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 GLN A 867 ASN B1018 HIS ** B1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.206620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.161337 restraints weight = 13479.658| |-----------------------------------------------------------------------------| r_work (start): 0.4172 rms_B_bonded: 3.47 r_work: 0.3631 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10440 Z= 0.136 Angle : 0.574 9.067 14150 Z= 0.287 Chirality : 0.042 0.167 1568 Planarity : 0.004 0.042 1849 Dihedral : 5.844 80.745 1398 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.15 % Allowed : 13.89 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.24), residues: 1274 helix: 1.35 (0.22), residues: 523 sheet: -0.27 (0.37), residues: 200 loop : -0.10 (0.28), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 586 TYR 0.011 0.001 TYR A 910 PHE 0.013 0.001 PHE A 283 TRP 0.016 0.001 TRP A 423 HIS 0.005 0.001 HIS A 713 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (10440) covalent geometry : angle 0.57439 / 0.29 (14150) hydrogen bonds : bond 0.03664 / 2.36 ( 491) hydrogen bonds : angle 4.52355 / 3.19 ( 1356) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 422 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7797 (mt0) REVERT: A 484 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8463 (tt) REVERT: A 647 TRP cc_start: 0.9136 (t60) cc_final: 0.8705 (t60) REVERT: A 709 TRP cc_start: 0.8489 (t-100) cc_final: 0.8041 (t60) REVERT: A 761 HIS cc_start: 0.7403 (p-80) cc_final: 0.7116 (p-80) REVERT: B 942 LYS cc_start: 0.9181 (ttmm) cc_final: 0.8790 (ttmm) REVERT: B 1022 LEU cc_start: 0.7747 (mt) cc_final: 0.7227 (tt) REVERT: B 1131 PHE cc_start: 0.7848 (OUTLIER) cc_final: 0.6498 (m-10) REVERT: B 1142 ILE cc_start: 0.8557 (mm) cc_final: 0.8293 (pt) outliers start: 24 outliers final: 13 residues processed: 133 average time/residue: 0.1131 time to fit residues: 20.8602 Evaluate side-chains 122 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain A residue 727 HIS Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain B residue 1131 PHE Chi-restraints excluded: chain B residue 1133 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 43 optimal weight: 0.8980 chunk 123 optimal weight: 0.0020 chunk 67 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 75 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 111 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 GLN B1063 GLN ** B1149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.207428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.162347 restraints weight = 13529.877| |-----------------------------------------------------------------------------| r_work (start): 0.4188 rms_B_bonded: 3.49 r_work: 0.3654 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10440 Z= 0.124 Angle : 0.560 9.002 14150 Z= 0.280 Chirality : 0.042 0.161 1568 Planarity : 0.004 0.040 1849 Dihedral : 5.725 80.762 1398 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.97 % Allowed : 14.61 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.24), residues: 1274 helix: 1.43 (0.22), residues: 523 sheet: -0.28 (0.37), residues: 200 loop : -0.08 (0.28), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1029 TYR 0.018 0.001 TYR B1094 PHE 0.011 0.001 PHE A 116 TRP 0.016 0.001 TRP A 714 HIS 0.009 0.001 HIS A 715 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (10440) covalent geometry : angle 0.56027 / 0.28 (14150) hydrogen bonds : bond 0.03475 / 2.23 ( 491) hydrogen bonds : angle 4.38744 / 3.10 ( 1356) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: A 422 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7741 (mt0) REVERT: A 484 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8497 (tt) REVERT: A 709 TRP cc_start: 0.8453 (t-100) cc_final: 0.8014 (t60) REVERT: A 761 HIS cc_start: 0.7442 (p-80) cc_final: 0.7159 (p-80) REVERT: A 844 MET cc_start: 0.7706 (tpp) cc_final: 0.7240 (tpp) REVERT: B 942 LYS cc_start: 0.9156 (ttmm) cc_final: 0.8823 (ttmm) REVERT: B 1022 LEU cc_start: 0.7766 (mt) cc_final: 0.7285 (tt) REVERT: B 1131 PHE cc_start: 0.7759 (OUTLIER) cc_final: 0.6410 (m-10) REVERT: B 1142 ILE cc_start: 0.8534 (mm) cc_final: 0.8275 (pt) outliers start: 22 outliers final: 14 residues processed: 130 average time/residue: 0.1108 time to fit residues: 19.8294 Evaluate side-chains 123 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 727 HIS Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain B residue 1063 GLN Chi-restraints excluded: chain B residue 1131 PHE Chi-restraints excluded: chain B residue 1133 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 36 optimal weight: 0.4980 chunk 66 optimal weight: 10.0000 chunk 119 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 GLN A 448 GLN B1063 GLN ** B1149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.196492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.138112 restraints weight = 13521.962| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 2.02 r_work: 0.3772 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10440 Z= 0.131 Angle : 0.572 8.982 14150 Z= 0.284 Chirality : 0.042 0.162 1568 Planarity : 0.004 0.041 1849 Dihedral : 5.683 81.120 1398 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.15 % Allowed : 14.87 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.24), residues: 1274 helix: 1.40 (0.22), residues: 524 sheet: -0.15 (0.39), residues: 182 loop : -0.17 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1029 TYR 0.010 0.001 TYR A 910 PHE 0.016 0.001 PHE B1265 TRP 0.016 0.002 TRP A 714 HIS 0.008 0.001 HIS A 715 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (10440) covalent geometry : angle 0.57171 / 0.28 (14150) hydrogen bonds : bond 0.03478 / 2.23 ( 491) hydrogen bonds : angle 4.37056 / 3.08 ( 1356) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 422 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7836 (mt0) REVERT: A 484 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8533 (tt) REVERT: A 709 TRP cc_start: 0.8717 (t-100) cc_final: 0.8201 (t60) REVERT: A 761 HIS cc_start: 0.7483 (p-80) cc_final: 0.7227 (p-80) REVERT: A 844 MET cc_start: 0.7767 (tpp) cc_final: 0.7371 (tpp) REVERT: A 859 MET cc_start: 0.7516 (mmp) cc_final: 0.7162 (mmm) REVERT: B 942 LYS cc_start: 0.9205 (ttmm) cc_final: 0.8820 (ttmm) REVERT: B 1022 LEU cc_start: 0.7837 (mt) cc_final: 0.7362 (tt) REVERT: B 1028 ARG cc_start: 0.3294 (OUTLIER) cc_final: 0.2451 (mmm-85) REVERT: B 1131 PHE cc_start: 0.7748 (OUTLIER) cc_final: 0.6433 (m-10) REVERT: B 1142 ILE cc_start: 0.8548 (mm) cc_final: 0.8287 (pt) outliers start: 24 outliers final: 14 residues processed: 132 average time/residue: 0.1128 time to fit residues: 20.4370 Evaluate side-chains 123 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain A residue 727 HIS Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain B residue 1028 ARG Chi-restraints excluded: chain B residue 1131 PHE Chi-restraints excluded: chain B residue 1133 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 36 optimal weight: 0.7980 chunk 75 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 26 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 22 optimal weight: 0.0010 chunk 63 optimal weight: 9.9990 chunk 95 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 68 optimal weight: 8.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 GLN ** B1149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.201521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 104)---------------| | r_work = 0.3901 r_free = 0.3901 target = 0.139295 restraints weight = 13655.573| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 2.24 r_work: 0.3806 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10440 Z= 0.118 Angle : 0.571 9.905 14150 Z= 0.281 Chirality : 0.041 0.156 1568 Planarity : 0.004 0.040 1849 Dihedral : 5.646 81.056 1398 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.79 % Allowed : 15.32 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.24), residues: 1274 helix: 1.50 (0.22), residues: 524 sheet: -0.26 (0.38), residues: 191 loop : -0.11 (0.28), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1029 TYR 0.020 0.001 TYR B1094 PHE 0.014 0.001 PHE B1265 TRP 0.017 0.001 TRP A 714 HIS 0.008 0.001 HIS A 715 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (10440) covalent geometry : angle 0.57129 / 0.28 (14150) hydrogen bonds : bond 0.03375 / 2.17 ( 491) hydrogen bonds : angle 4.32147 / 3.05 ( 1356) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: A 256 MET cc_start: 0.6895 (mmt) cc_final: 0.6439 (mmt) REVERT: A 484 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8517 (tt) REVERT: A 709 TRP cc_start: 0.8720 (t-100) cc_final: 0.8209 (t60) REVERT: A 761 HIS cc_start: 0.7500 (p-80) cc_final: 0.7234 (p-80) REVERT: A 859 MET cc_start: 0.7533 (mmp) cc_final: 0.7197 (mmm) REVERT: B 942 LYS cc_start: 0.9185 (ttmm) cc_final: 0.8842 (ttmm) REVERT: B 1022 LEU cc_start: 0.7851 (mt) cc_final: 0.7381 (tt) REVERT: B 1028 ARG cc_start: 0.3149 (OUTLIER) cc_final: 0.2344 (mmm-85) REVERT: B 1131 PHE cc_start: 0.7606 (OUTLIER) cc_final: 0.6522 (m-10) REVERT: B 1142 ILE cc_start: 0.8503 (mm) cc_final: 0.8262 (pt) outliers start: 20 outliers final: 14 residues processed: 121 average time/residue: 0.1117 time to fit residues: 18.4525 Evaluate side-chains 120 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain A residue 727 HIS Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain B residue 1028 ARG Chi-restraints excluded: chain B residue 1131 PHE Chi-restraints excluded: chain B residue 1133 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 72 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 107 optimal weight: 0.0000 chunk 103 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 69 optimal weight: 8.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 2 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.200157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.140856 restraints weight = 13708.708| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 2.24 r_work: 0.3782 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3618 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10440 Z= 0.148 Angle : 0.591 9.749 14150 Z= 0.292 Chirality : 0.042 0.195 1568 Planarity : 0.004 0.040 1849 Dihedral : 5.659 82.558 1398 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.88 % Allowed : 15.41 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.24), residues: 1274 helix: 1.39 (0.22), residues: 530 sheet: -0.39 (0.38), residues: 192 loop : -0.19 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1029 TYR 0.009 0.001 TYR A 910 PHE 0.013 0.001 PHE B1265 TRP 0.017 0.002 TRP A 647 HIS 0.008 0.001 HIS A 715 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (10440) covalent geometry : angle 0.59126 / 0.29 (14150) hydrogen bonds : bond 0.03515 / 2.26 ( 491) hydrogen bonds : angle 4.36042 / 3.08 ( 1356) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: A 484 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8541 (tt) REVERT: A 709 TRP cc_start: 0.8718 (t-100) cc_final: 0.8225 (t60) REVERT: A 761 HIS cc_start: 0.7457 (p-80) cc_final: 0.7248 (p-80) REVERT: A 859 MET cc_start: 0.7538 (mmp) cc_final: 0.7201 (mmm) REVERT: B 1022 LEU cc_start: 0.7787 (mt) cc_final: 0.7412 (tt) REVERT: B 1028 ARG cc_start: 0.3282 (OUTLIER) cc_final: 0.2450 (mmm-85) REVERT: B 1131 PHE cc_start: 0.7570 (OUTLIER) cc_final: 0.6652 (m-10) REVERT: B 1142 ILE cc_start: 0.8496 (mm) cc_final: 0.8269 (pt) outliers start: 21 outliers final: 13 residues processed: 122 average time/residue: 0.1046 time to fit residues: 17.7503 Evaluate side-chains 118 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain A residue 727 HIS Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain B residue 1028 ARG Chi-restraints excluded: chain B residue 1131 PHE Chi-restraints excluded: chain B residue 1133 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 59 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 97 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 99 optimal weight: 8.9990 chunk 96 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 GLN ** B1149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.202399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.137700 restraints weight = 13624.423| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 2.22 r_work: 0.3752 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10440 Z= 0.146 Angle : 0.584 8.843 14150 Z= 0.288 Chirality : 0.042 0.173 1568 Planarity : 0.004 0.040 1849 Dihedral : 5.667 83.879 1398 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.61 % Allowed : 16.04 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.24), residues: 1274 helix: 1.46 (0.22), residues: 524 sheet: -0.44 (0.38), residues: 192 loop : -0.17 (0.28), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A1029 TYR 0.021 0.001 TYR B1094 PHE 0.013 0.001 PHE B1265 TRP 0.017 0.002 TRP A 647 HIS 0.007 0.001 HIS A 715 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (10440) covalent geometry : angle 0.58422 / 0.29 (14150) hydrogen bonds : bond 0.03449 / 2.23 ( 491) hydrogen bonds : angle 4.34159 / 3.06 ( 1356) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: A 256 MET cc_start: 0.6980 (mmt) cc_final: 0.6577 (mmt) REVERT: A 484 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8500 (tt) REVERT: A 709 TRP cc_start: 0.8569 (t-100) cc_final: 0.8166 (t60) REVERT: A 761 HIS cc_start: 0.7497 (p-80) cc_final: 0.7255 (p-80) REVERT: A 859 MET cc_start: 0.7533 (mmp) cc_final: 0.7202 (mmm) REVERT: B 1022 LEU cc_start: 0.7697 (mt) cc_final: 0.7389 (tt) REVERT: B 1028 ARG cc_start: 0.3204 (OUTLIER) cc_final: 0.2448 (mmm-85) REVERT: B 1110 GLN cc_start: 0.8746 (pt0) cc_final: 0.8475 (pt0) REVERT: B 1131 PHE cc_start: 0.7511 (OUTLIER) cc_final: 0.6736 (m-10) REVERT: B 1142 ILE cc_start: 0.8495 (mm) cc_final: 0.8277 (pt) outliers start: 18 outliers final: 15 residues processed: 113 average time/residue: 0.1114 time to fit residues: 17.6279 Evaluate side-chains 116 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain A residue 727 HIS Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain B residue 1028 ARG Chi-restraints excluded: chain B residue 1131 PHE Chi-restraints excluded: chain B residue 1133 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 83 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 chunk 98 optimal weight: 5.9990 chunk 87 optimal weight: 0.5980 chunk 107 optimal weight: 0.0980 chunk 99 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 94 optimal weight: 0.2980 chunk 86 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 115 optimal weight: 5.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 GLN ** B1149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.204031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.139758 restraints weight = 13868.902| |-----------------------------------------------------------------------------| r_work (start): 0.4044 rms_B_bonded: 2.23 r_work: 0.3869 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3700 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10440 Z= 0.110 Angle : 0.570 9.541 14150 Z= 0.279 Chirality : 0.041 0.146 1568 Planarity : 0.004 0.040 1849 Dihedral : 5.599 83.457 1398 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.88 % Allowed : 15.86 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.24), residues: 1274 helix: 1.58 (0.22), residues: 520 sheet: -0.39 (0.38), residues: 192 loop : -0.19 (0.28), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A1029 TYR 0.010 0.001 TYR A 910 PHE 0.011 0.001 PHE B1265 TRP 0.017 0.001 TRP A 647 HIS 0.006 0.001 HIS A 715 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (10440) covalent geometry : angle 0.56994 / 0.28 (14150) hydrogen bonds : bond 0.03206 / 2.07 ( 491) hydrogen bonds : angle 4.24457 / 3.00 ( 1356) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2943.16 seconds wall clock time: 51 minutes 5.41 seconds (3065.41 seconds total)