Starting phenix.real_space_refine on Sun Apr 7 02:59:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vxa_43615/04_2024/8vxa_43615.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vxa_43615/04_2024/8vxa_43615.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vxa_43615/04_2024/8vxa_43615.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vxa_43615/04_2024/8vxa_43615.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vxa_43615/04_2024/8vxa_43615.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vxa_43615/04_2024/8vxa_43615.pdb" } resolution = 2.79 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= 0.001 sd= 0.020 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 24 5.49 5 S 27 5.16 5 C 5877 2.51 5 N 1685 2.21 5 O 1818 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9431 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 284 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "C" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 201 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 8946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1139, 8946 Classifications: {'peptide': 1139} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 45, 'TRANS': 1089} Chain breaks: 1 Time building chain proxies: 5.55, per 1000 atoms: 0.59 Number of scatterers: 9431 At special positions: 0 Unit cell: (89.2, 92.545, 112.615, 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 27 16.00 P 24 15.00 O 1818 8.00 N 1685 7.00 C 5877 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 3.6 seconds 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2120 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 3 sheets defined 60.2% alpha, 7.5% beta 6 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 3.36 Creating SS restraints... Processing helix chain 'A' and resid 4 through 16 Processing helix chain 'A' and resid 23 through 33 Processing helix chain 'A' and resid 50 through 72 Processing helix chain 'A' and resid 75 through 95 removed outlier: 3.735A pdb=" N ALA A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 118 Processing helix chain 'A' and resid 120 through 129 Processing helix chain 'A' and resid 138 through 150 Processing helix chain 'A' and resid 151 through 166 removed outlier: 3.842A pdb=" N ASP A 157 " --> pdb=" O ARG A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 224 Processing helix chain 'A' and resid 225 through 247 removed outlier: 3.883A pdb=" N LEU A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 267 removed outlier: 3.859A pdb=" N HIS A 260 " --> pdb=" O PHE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 274 Processing helix chain 'A' and resid 285 through 299 Processing helix chain 'A' and resid 311 through 319 removed outlier: 4.220A pdb=" N VAL A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 348 removed outlier: 3.960A pdb=" N ILE A 338 " --> pdb=" O GLY A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 375 removed outlier: 3.504A pdb=" N ALA A 368 " --> pdb=" O ALA A 364 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR A 369 " --> pdb=" O GLN A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 401 removed outlier: 4.537A pdb=" N ASP A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 418 removed outlier: 3.636A pdb=" N ALA A 414 " --> pdb=" O LYS A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 423 Processing helix chain 'A' and resid 439 through 454 Processing helix chain 'A' and resid 457 through 461 Processing helix chain 'A' and resid 475 through 483 Processing helix chain 'A' and resid 553 through 567 Processing helix chain 'A' and resid 578 through 580 No H-bonds generated for 'chain 'A' and resid 578 through 580' Processing helix chain 'A' and resid 581 through 595 removed outlier: 3.811A pdb=" N PHE A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA A 586 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU A 587 " --> pdb=" O GLU A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 608 Processing helix chain 'A' and resid 609 through 618 removed outlier: 3.686A pdb=" N GLU A 618 " --> pdb=" O SER A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 632 removed outlier: 3.517A pdb=" N LEU A 632 " --> pdb=" O ALA A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 655 Processing helix chain 'A' and resid 665 through 668 Processing helix chain 'A' and resid 691 through 700 Processing helix chain 'A' and resid 720 through 733 Processing helix chain 'A' and resid 742 through 760 removed outlier: 4.069A pdb=" N ARG A 754 " --> pdb=" O VAL A 750 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET A 755 " --> pdb=" O LEU A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 773 Processing helix chain 'A' and resid 786 through 813 Processing helix chain 'A' and resid 818 through 820 No H-bonds generated for 'chain 'A' and resid 818 through 820' Processing helix chain 'A' and resid 821 through 830 Processing helix chain 'A' and resid 833 through 840 Processing helix chain 'A' and resid 844 through 865 removed outlier: 3.821A pdb=" N LYS A 852 " --> pdb=" O ARG A 848 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG A 865 " --> pdb=" O TYR A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 878 Processing helix chain 'A' and resid 880 through 890 Processing helix chain 'A' and resid 890 through 907 removed outlier: 4.403A pdb=" N GLN A 896 " --> pdb=" O ALA A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 925 removed outlier: 4.064A pdb=" N ILE A 917 " --> pdb=" O ALA A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 949 Processing helix chain 'A' and resid 951 through 955 removed outlier: 3.601A pdb=" N VAL A 955 " --> pdb=" O MET A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 971 Processing helix chain 'A' and resid 973 through 990 Processing helix chain 'A' and resid 993 through 1002 removed outlier: 3.863A pdb=" N THR A 998 " --> pdb=" O GLY A 994 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N THR A 999 " --> pdb=" O ASP A 995 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A1000 " --> pdb=" O THR A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1015 removed outlier: 3.762A pdb=" N ALA A1011 " --> pdb=" O PHE A1007 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A1012 " --> pdb=" O ALA A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1028 removed outlier: 3.727A pdb=" N GLY A1028 " --> pdb=" O LEU A1024 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1043 Processing helix chain 'A' and resid 1048 through 1058 Processing helix chain 'A' and resid 1058 through 1067 removed outlier: 3.767A pdb=" N ILE A1062 " --> pdb=" O SER A1058 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1086 removed outlier: 3.740A pdb=" N LEU A1080 " --> pdb=" O ARG A1076 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLU A1081 " --> pdb=" O VAL A1077 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE A1082 " --> pdb=" O MET A1078 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 381 through 383 removed outlier: 3.657A pdb=" N VAL A 405 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE A 428 " --> pdb=" O VAL A 464 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N LEU A 466 " --> pdb=" O PHE A 428 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N PHE A 430 " --> pdb=" O LEU A 466 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU A 325 " --> pdb=" O CYS A 465 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N SER A 467 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL A 327 " --> pdb=" O SER A 467 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 525 through 531 removed outlier: 4.845A pdb=" N TRP A 525 " --> pdb=" O LEU A 517 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU A 517 " --> pdb=" O TRP A 525 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N SER A 527 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LEU A 515 " --> pdb=" O SER A 527 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLY A 513 " --> pdb=" O PHE A 529 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ARG A 500 " --> pdb=" O GLY A 711 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N VAL A 713 " --> pdb=" O ARG A 500 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLN A 502 " --> pdb=" O VAL A 713 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N TYR A 715 " --> pdb=" O GLN A 502 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY A 504 " --> pdb=" O TYR A 715 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ILE A 717 " --> pdb=" O GLY A 504 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N VAL A 506 " --> pdb=" O ILE A 717 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL A 572 " --> pdb=" O THR A 661 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N SER A 663 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE A 574 " --> pdb=" O SER A 663 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1097 through 1102 removed outlier: 3.623A pdb=" N TYR A1099 " --> pdb=" O PHE A1163 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N LEU A1150 " --> pdb=" O LEU A1118 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU A1118 " --> pdb=" O LEU A1150 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL A1152 " --> pdb=" O LEU A1116 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N HIS A1125 " --> pdb=" O ILE A1138 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY A1136 " --> pdb=" O VAL A1127 " (cutoff:3.500A) 484 hydrogen bonds defined for protein. 1422 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 15 hydrogen bonds 30 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 4.24 Time building geometry restraints manager: 5.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2848 1.33 - 1.45: 1445 1.45 - 1.57: 5278 1.57 - 1.69: 46 1.69 - 1.80: 46 Bond restraints: 9663 Sorted by residual: bond pdb=" C3' DC C 6 " pdb=" O3' DC C 6 " ideal model delta sigma weight residual 1.422 1.458 -0.036 3.00e-02 1.11e+03 1.48e+00 bond pdb=" C3' DT C 5 " pdb=" O3' DT C 5 " ideal model delta sigma weight residual 1.422 1.456 -0.034 3.00e-02 1.11e+03 1.29e+00 bond pdb=" CG1 ILE A 566 " pdb=" CD1 ILE A 566 " ideal model delta sigma weight residual 1.513 1.472 0.041 3.90e-02 6.57e+02 1.09e+00 bond pdb=" CB GLU A 980 " pdb=" CG GLU A 980 " ideal model delta sigma weight residual 1.520 1.489 0.031 3.00e-02 1.11e+03 1.06e+00 bond pdb=" CA ILE A 388 " pdb=" CB ILE A 388 " ideal model delta sigma weight residual 1.550 1.540 0.010 1.03e-02 9.43e+03 9.97e-01 ... (remaining 9658 not shown) Histogram of bond angle deviations from ideal: 100.10 - 106.91: 415 106.91 - 113.71: 5361 113.71 - 120.52: 3872 120.52 - 127.32: 3427 127.32 - 134.13: 144 Bond angle restraints: 13219 Sorted by residual: angle pdb=" N GLY A 760 " pdb=" CA GLY A 760 " pdb=" C GLY A 760 " ideal model delta sigma weight residual 110.58 114.65 -4.07 1.35e+00 5.49e-01 9.11e+00 angle pdb=" C GLU A 768 " pdb=" N TYR A 769 " pdb=" CA TYR A 769 " ideal model delta sigma weight residual 120.44 124.14 -3.70 1.30e+00 5.92e-01 8.12e+00 angle pdb=" CA LEU A1135 " pdb=" CB LEU A1135 " pdb=" CG LEU A1135 " ideal model delta sigma weight residual 116.30 126.00 -9.70 3.50e+00 8.16e-02 7.69e+00 angle pdb=" N LEU A 427 " pdb=" CA LEU A 427 " pdb=" C LEU A 427 " ideal model delta sigma weight residual 108.32 111.93 -3.61 1.64e+00 3.72e-01 4.84e+00 angle pdb=" C3' DT C 5 " pdb=" O3' DT C 5 " pdb=" P DC C 6 " ideal model delta sigma weight residual 120.20 123.36 -3.16 1.50e+00 4.44e-01 4.45e+00 ... (remaining 13214 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.73: 5401 25.73 - 51.47: 305 51.47 - 77.20: 46 77.20 - 102.94: 5 102.94 - 128.67: 1 Dihedral angle restraints: 5758 sinusoidal: 2477 harmonic: 3281 Sorted by residual: dihedral pdb=" C4' DC C 6 " pdb=" C3' DC C 6 " pdb=" O3' DC C 6 " pdb=" P DC C 7 " ideal model delta sinusoidal sigma weight residual 220.00 91.33 128.67 1 3.50e+01 8.16e-04 1.27e+01 dihedral pdb=" CA ILE A 662 " pdb=" C ILE A 662 " pdb=" N SER A 663 " pdb=" CA SER A 663 " ideal model delta harmonic sigma weight residual 180.00 -162.70 -17.30 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA ASN A 672 " pdb=" C ASN A 672 " pdb=" N LEU A 673 " pdb=" CA LEU A 673 " ideal model delta harmonic sigma weight residual 180.00 163.14 16.86 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 5755 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 887 0.027 - 0.054: 395 0.054 - 0.082: 129 0.082 - 0.109: 74 0.109 - 0.136: 16 Chirality restraints: 1501 Sorted by residual: chirality pdb=" CA ILE A 817 " pdb=" N ILE A 817 " pdb=" C ILE A 817 " pdb=" CB ILE A 817 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" CA ILE A 381 " pdb=" N ILE A 381 " pdb=" C ILE A 381 " pdb=" CB ILE A 381 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 chirality pdb=" CA VAL A 526 " pdb=" N VAL A 526 " pdb=" C VAL A 526 " pdb=" CB VAL A 526 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.70e-01 ... (remaining 1498 not shown) Planarity restraints: 1638 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 35 " 0.025 2.00e-02 2.50e+03 2.15e-02 1.15e+01 pdb=" CG TRP A 35 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP A 35 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP A 35 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 35 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 35 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 35 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 35 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 35 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 35 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 563 " -0.012 2.00e-02 2.50e+03 1.27e-02 4.06e+00 pdb=" CG TRP A 563 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP A 563 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP A 563 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 563 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 563 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 563 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 563 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 563 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 563 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 375 " -0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO A 376 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 376 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 376 " -0.024 5.00e-02 4.00e+02 ... (remaining 1635 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 946 2.74 - 3.28: 9537 3.28 - 3.82: 16768 3.82 - 4.36: 19865 4.36 - 4.90: 32995 Nonbonded interactions: 80111 Sorted by model distance: nonbonded pdb=" OE2 GLU A 395 " pdb=" OH TYR A1003 " model vdw 2.204 2.440 nonbonded pdb=" OG1 THR A 357 " pdb=" OG SER A 363 " model vdw 2.250 2.440 nonbonded pdb=" OE1 GLU A 304 " pdb=" NH2 ARG A 337 " model vdw 2.251 2.520 nonbonded pdb=" NH1 ARG A 454 " pdb=" O ASP A 828 " model vdw 2.272 2.520 nonbonded pdb=" NH2 ARG A 685 " pdb=" OE1 GLU A 694 " model vdw 2.275 2.520 ... (remaining 80106 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: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.850 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 37.590 Find NCS groups from input model: 0.270 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: 0.010 Load rotamer database and sin/cos tables:14.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 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 0.041 9663 Z= 0.221 Angle : 0.532 9.703 13219 Z= 0.294 Chirality : 0.039 0.136 1501 Planarity : 0.004 0.043 1638 Dihedral : 15.673 128.673 3638 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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 (0.25), residues: 1135 helix: 1.12 (0.21), residues: 626 sheet: 0.12 (0.64), residues: 79 loop : -0.54 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A 35 HIS 0.004 0.001 HIS A 260 PHE 0.023 0.002 PHE A 413 TYR 0.013 0.001 TYR A 445 ARG 0.003 0.000 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 PHE cc_start: 0.8083 (t80) cc_final: 0.7798 (t80) REVERT: A 153 ARG cc_start: 0.7431 (ttm-80) cc_final: 0.7157 (mtt180) REVERT: A 264 ASP cc_start: 0.7024 (p0) cc_final: 0.6809 (p0) REVERT: A 322 ASN cc_start: 0.7133 (t0) cc_final: 0.6886 (t0) REVERT: A 382 SER cc_start: 0.7641 (m) cc_final: 0.7420 (t) REVERT: A 383 MET cc_start: 0.7155 (ttt) cc_final: 0.6864 (ttp) REVERT: A 472 ASP cc_start: 0.6824 (m-30) cc_final: 0.6347 (m-30) REVERT: A 548 LYS cc_start: 0.7909 (mtmm) cc_final: 0.7468 (mtmm) REVERT: A 649 ILE cc_start: 0.7968 (tt) cc_final: 0.7610 (pt) REVERT: A 709 VAL cc_start: 0.8683 (p) cc_final: 0.8418 (t) REVERT: A 764 LYS cc_start: 0.6737 (tptt) cc_final: 0.6404 (tptt) REVERT: A 819 ASP cc_start: 0.6905 (t70) cc_final: 0.6683 (t0) REVERT: A 831 GLN cc_start: 0.7262 (tp-100) cc_final: 0.6985 (mm-40) REVERT: A 1169 ASP cc_start: 0.7219 (t0) cc_final: 0.6970 (t70) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 1.3409 time to fit residues: 341.7677 Evaluate side-chains 194 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 90 optimal weight: 0.0070 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 overall best weight: 0.6402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 495 ASN A 669 GLN A 772 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9663 Z= 0.257 Angle : 0.555 10.086 13219 Z= 0.297 Chirality : 0.041 0.147 1501 Planarity : 0.005 0.051 1638 Dihedral : 15.022 133.432 1522 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.64 % Allowed : 10.55 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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 (0.25), residues: 1135 helix: 1.23 (0.21), residues: 640 sheet: -0.51 (0.63), residues: 77 loop : -0.66 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 35 HIS 0.006 0.001 HIS A 260 PHE 0.024 0.002 PHE A 413 TYR 0.012 0.002 TYR A 125 ARG 0.006 0.001 ARG A 758 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 199 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ILE cc_start: 0.7546 (pt) cc_final: 0.7321 (pp) REVERT: A 264 ASP cc_start: 0.7014 (p0) cc_final: 0.6781 (p0) REVERT: A 322 ASN cc_start: 0.7163 (t0) cc_final: 0.6888 (t0) REVERT: A 383 MET cc_start: 0.7062 (ttt) cc_final: 0.6749 (ttp) REVERT: A 649 ILE cc_start: 0.8028 (tt) cc_final: 0.7573 (pt) REVERT: A 671 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8198 (tt) REVERT: A 709 VAL cc_start: 0.8692 (p) cc_final: 0.8405 (t) REVERT: A 740 MET cc_start: 0.8110 (mmm) cc_final: 0.7434 (mmm) REVERT: A 768 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.6667 (mp0) REVERT: A 819 ASP cc_start: 0.6900 (t70) cc_final: 0.6648 (t0) REVERT: A 831 GLN cc_start: 0.7240 (tp-100) cc_final: 0.6970 (mm-40) REVERT: A 836 GLN cc_start: 0.7397 (tt0) cc_final: 0.7127 (tt0) REVERT: A 1029 PHE cc_start: 0.6502 (OUTLIER) cc_final: 0.5351 (m-80) REVERT: A 1169 ASP cc_start: 0.7135 (t0) cc_final: 0.6926 (t0) outliers start: 25 outliers final: 8 residues processed: 208 average time/residue: 1.3412 time to fit residues: 298.0096 Evaluate side-chains 199 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 188 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 399 ARG Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 669 GLN Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1121 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 28 optimal weight: 0.4980 chunk 104 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 93 optimal weight: 0.0030 chunk 103 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 ASN A 772 ASN A 815 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9663 Z= 0.213 Angle : 0.529 9.688 13219 Z= 0.282 Chirality : 0.040 0.146 1501 Planarity : 0.004 0.050 1638 Dihedral : 14.978 133.975 1522 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.43 % Allowed : 13.92 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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: 0.75 (0.25), residues: 1135 helix: 1.38 (0.21), residues: 638 sheet: -0.55 (0.61), residues: 77 loop : -0.60 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 35 HIS 0.005 0.001 HIS A 260 PHE 0.016 0.001 PHE A 413 TYR 0.012 0.001 TYR A 445 ARG 0.008 0.000 ARG A 758 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 197 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ILE cc_start: 0.7582 (pt) cc_final: 0.7340 (pp) REVERT: A 151 ASP cc_start: 0.6600 (t70) cc_final: 0.6341 (t0) REVERT: A 235 LYS cc_start: 0.6970 (OUTLIER) cc_final: 0.6742 (ttmm) REVERT: A 264 ASP cc_start: 0.7009 (p0) cc_final: 0.6737 (p0) REVERT: A 322 ASN cc_start: 0.7170 (t0) cc_final: 0.6911 (t0) REVERT: A 548 LYS cc_start: 0.7890 (mtmm) cc_final: 0.7606 (mtmm) REVERT: A 552 SER cc_start: 0.8189 (t) cc_final: 0.7917 (p) REVERT: A 649 ILE cc_start: 0.8008 (tt) cc_final: 0.7555 (pt) REVERT: A 709 VAL cc_start: 0.8728 (p) cc_final: 0.8438 (t) REVERT: A 740 MET cc_start: 0.8071 (mmm) cc_final: 0.7470 (mmm) REVERT: A 768 GLU cc_start: 0.6901 (mp0) cc_final: 0.6631 (mp0) REVERT: A 814 GLU cc_start: 0.6415 (tp30) cc_final: 0.6097 (tp30) REVERT: A 819 ASP cc_start: 0.6872 (t70) cc_final: 0.6631 (t0) REVERT: A 831 GLN cc_start: 0.7247 (tp-100) cc_final: 0.6974 (mm-40) REVERT: A 836 GLN cc_start: 0.7461 (tt0) cc_final: 0.7185 (tt0) REVERT: A 897 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7236 (mm) REVERT: A 1029 PHE cc_start: 0.6786 (OUTLIER) cc_final: 0.5708 (m-80) outliers start: 23 outliers final: 14 residues processed: 206 average time/residue: 1.3729 time to fit residues: 300.9718 Evaluate side-chains 195 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 178 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1151 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 54 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 70 optimal weight: 0.0000 chunk 104 optimal weight: 0.7980 chunk 111 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 92 optimal weight: 0.7980 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 ASN A 815 ASN A1125 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9663 Z= 0.217 Angle : 0.521 9.602 13219 Z= 0.278 Chirality : 0.039 0.148 1501 Planarity : 0.004 0.045 1638 Dihedral : 14.977 134.259 1522 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.38 % Allowed : 14.98 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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: 0.80 (0.25), residues: 1135 helix: 1.44 (0.21), residues: 636 sheet: -0.89 (0.58), residues: 86 loop : -0.51 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 35 HIS 0.006 0.001 HIS A1125 PHE 0.019 0.001 PHE A 966 TYR 0.023 0.002 TYR A 445 ARG 0.010 0.000 ARG A 758 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 192 time to evaluate : 1.046 Fit side-chains REVERT: A 94 ILE cc_start: 0.7650 (pt) cc_final: 0.7390 (pp) REVERT: A 151 ASP cc_start: 0.6603 (t70) cc_final: 0.6322 (t0) REVERT: A 235 LYS cc_start: 0.7061 (OUTLIER) cc_final: 0.6822 (ttmm) REVERT: A 264 ASP cc_start: 0.6990 (p0) cc_final: 0.6723 (p0) REVERT: A 322 ASN cc_start: 0.7167 (t0) cc_final: 0.6906 (t0) REVERT: A 445 TYR cc_start: 0.8155 (t80) cc_final: 0.7911 (t80) REVERT: A 548 LYS cc_start: 0.7887 (mtmm) cc_final: 0.7578 (mtmm) REVERT: A 552 SER cc_start: 0.8195 (t) cc_final: 0.7951 (p) REVERT: A 671 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8180 (tt) REVERT: A 709 VAL cc_start: 0.8772 (p) cc_final: 0.8470 (t) REVERT: A 740 MET cc_start: 0.8120 (mmm) cc_final: 0.7507 (mmm) REVERT: A 768 GLU cc_start: 0.6975 (mp0) cc_final: 0.6676 (mp0) REVERT: A 814 GLU cc_start: 0.6376 (tp30) cc_final: 0.6138 (tp30) REVERT: A 819 ASP cc_start: 0.6839 (t70) cc_final: 0.6611 (t0) REVERT: A 831 GLN cc_start: 0.7254 (tp-100) cc_final: 0.7008 (mm-40) REVERT: A 1029 PHE cc_start: 0.6777 (OUTLIER) cc_final: 0.5669 (m-80) REVERT: A 1102 MET cc_start: 0.5368 (tpp) cc_final: 0.5137 (tpp) outliers start: 32 outliers final: 16 residues processed: 203 average time/residue: 1.3550 time to fit residues: 292.6497 Evaluate side-chains 205 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 186 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 399 ARG Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1151 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 99 optimal weight: 0.0980 chunk 28 optimal weight: 0.0980 chunk 37 optimal weight: 2.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 HIS A 686 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9663 Z= 0.195 Angle : 0.508 9.342 13219 Z= 0.272 Chirality : 0.039 0.151 1501 Planarity : 0.004 0.045 1638 Dihedral : 14.962 134.539 1522 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.48 % Allowed : 16.03 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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: 0.93 (0.25), residues: 1135 helix: 1.54 (0.21), residues: 639 sheet: -0.52 (0.55), residues: 97 loop : -0.53 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 35 HIS 0.005 0.001 HIS A 260 PHE 0.015 0.001 PHE A 779 TYR 0.021 0.002 TYR A 445 ARG 0.010 0.000 ARG A 758 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 197 time to evaluate : 0.867 Fit side-chains revert: symmetry clash REVERT: A 94 ILE cc_start: 0.7653 (pt) cc_final: 0.7392 (pp) REVERT: A 151 ASP cc_start: 0.6753 (t70) cc_final: 0.6429 (t0) REVERT: A 235 LYS cc_start: 0.7056 (OUTLIER) cc_final: 0.6819 (ttmm) REVERT: A 264 ASP cc_start: 0.6974 (p0) cc_final: 0.6710 (p0) REVERT: A 322 ASN cc_start: 0.7162 (t0) cc_final: 0.6907 (t0) REVERT: A 445 TYR cc_start: 0.8182 (t80) cc_final: 0.7937 (t80) REVERT: A 548 LYS cc_start: 0.7868 (mtmm) cc_final: 0.7549 (mtmm) REVERT: A 671 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8120 (tt) REVERT: A 695 PHE cc_start: 0.8068 (t80) cc_final: 0.7867 (t80) REVERT: A 740 MET cc_start: 0.8082 (mmm) cc_final: 0.7506 (mmm) REVERT: A 819 ASP cc_start: 0.6842 (t70) cc_final: 0.6613 (t0) REVERT: A 831 GLN cc_start: 0.7270 (tp-100) cc_final: 0.7013 (mm-40) REVERT: A 897 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7242 (mm) REVERT: A 979 MET cc_start: 0.8145 (mtm) cc_final: 0.7825 (mtm) REVERT: A 989 ASN cc_start: 0.7724 (OUTLIER) cc_final: 0.7490 (t0) REVERT: A 1018 SER cc_start: 0.7499 (m) cc_final: 0.7214 (p) REVERT: A 1029 PHE cc_start: 0.6631 (OUTLIER) cc_final: 0.5538 (m-80) REVERT: A 1102 MET cc_start: 0.5327 (tpp) cc_final: 0.5123 (tpp) outliers start: 33 outliers final: 13 residues processed: 213 average time/residue: 1.3492 time to fit residues: 307.0755 Evaluate side-chains 208 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 190 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 399 ARG Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1121 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 92 optimal weight: 0.0270 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 0.0870 chunk 58 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1125 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9663 Z= 0.241 Angle : 0.530 9.486 13219 Z= 0.283 Chirality : 0.040 0.162 1501 Planarity : 0.005 0.049 1638 Dihedral : 15.010 135.348 1522 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.16 % Allowed : 17.93 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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: 0.86 (0.25), residues: 1135 helix: 1.47 (0.21), residues: 642 sheet: -0.58 (0.53), residues: 97 loop : -0.54 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 35 HIS 0.007 0.001 HIS A1125 PHE 0.016 0.001 PHE A 779 TYR 0.018 0.002 TYR A 445 ARG 0.012 0.000 ARG A 758 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 196 time to evaluate : 0.997 Fit side-chains revert: symmetry clash REVERT: A 94 ILE cc_start: 0.7494 (pt) cc_final: 0.7216 (pp) REVERT: A 151 ASP cc_start: 0.6823 (t70) cc_final: 0.6462 (t0) REVERT: A 235 LYS cc_start: 0.7056 (OUTLIER) cc_final: 0.6814 (ttmm) REVERT: A 264 ASP cc_start: 0.6978 (p0) cc_final: 0.6720 (p0) REVERT: A 266 TRP cc_start: 0.6795 (t-100) cc_final: 0.6394 (t-100) REVERT: A 322 ASN cc_start: 0.7166 (t0) cc_final: 0.6902 (t0) REVERT: A 445 TYR cc_start: 0.8183 (t80) cc_final: 0.7924 (t80) REVERT: A 548 LYS cc_start: 0.7862 (mtmm) cc_final: 0.7579 (mtmm) REVERT: A 671 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8174 (tt) REVERT: A 692 VAL cc_start: 0.7773 (t) cc_final: 0.7565 (t) REVERT: A 740 MET cc_start: 0.8081 (mmm) cc_final: 0.7537 (mmm) REVERT: A 819 ASP cc_start: 0.6893 (t70) cc_final: 0.6664 (t0) REVERT: A 831 GLN cc_start: 0.7260 (tp-100) cc_final: 0.7043 (mm-40) REVERT: A 979 MET cc_start: 0.8159 (mtm) cc_final: 0.7860 (mtm) REVERT: A 989 ASN cc_start: 0.7741 (OUTLIER) cc_final: 0.7501 (t0) REVERT: A 1029 PHE cc_start: 0.6456 (OUTLIER) cc_final: 0.5303 (m-80) outliers start: 30 outliers final: 17 residues processed: 210 average time/residue: 1.3477 time to fit residues: 302.0954 Evaluate side-chains 211 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 190 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 399 ARG Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1121 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 62 optimal weight: 0.0070 chunk 93 optimal weight: 0.0980 chunk 110 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 67 optimal weight: 0.4980 chunk 51 optimal weight: 0.0010 chunk 68 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 overall best weight: 0.2604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9663 Z= 0.165 Angle : 0.510 8.790 13219 Z= 0.271 Chirality : 0.038 0.154 1501 Planarity : 0.004 0.052 1638 Dihedral : 14.930 136.156 1522 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.74 % Allowed : 18.67 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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: 1135 helix: 1.67 (0.21), residues: 643 sheet: -0.49 (0.55), residues: 95 loop : -0.54 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 525 HIS 0.005 0.001 HIS A 116 PHE 0.016 0.001 PHE A 779 TYR 0.019 0.001 TYR A 445 ARG 0.011 0.000 ARG A 758 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 195 time to evaluate : 0.983 Fit side-chains REVERT: A 94 ILE cc_start: 0.7457 (pt) cc_final: 0.7171 (pp) REVERT: A 151 ASP cc_start: 0.6818 (t70) cc_final: 0.6505 (t0) REVERT: A 235 LYS cc_start: 0.6992 (OUTLIER) cc_final: 0.6734 (ttmm) REVERT: A 264 ASP cc_start: 0.6988 (p0) cc_final: 0.6719 (p0) REVERT: A 266 TRP cc_start: 0.6638 (t-100) cc_final: 0.6204 (t-100) REVERT: A 322 ASN cc_start: 0.7160 (t0) cc_final: 0.6901 (t0) REVERT: A 525 TRP cc_start: 0.6474 (p90) cc_final: 0.6255 (p90) REVERT: A 544 LYS cc_start: 0.7776 (mttp) cc_final: 0.7571 (mttt) REVERT: A 548 LYS cc_start: 0.7846 (mtmm) cc_final: 0.7404 (mtmm) REVERT: A 549 MET cc_start: 0.7170 (mmm) cc_final: 0.6919 (mmm) REVERT: A 692 VAL cc_start: 0.7766 (t) cc_final: 0.7565 (t) REVERT: A 740 MET cc_start: 0.8079 (mmm) cc_final: 0.7489 (mmm) REVERT: A 819 ASP cc_start: 0.6848 (t70) cc_final: 0.6623 (t0) REVERT: A 831 GLN cc_start: 0.7270 (tp-100) cc_final: 0.6978 (mm-40) REVERT: A 897 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7157 (mm) REVERT: A 989 ASN cc_start: 0.7663 (OUTLIER) cc_final: 0.7424 (t0) REVERT: A 1018 SER cc_start: 0.7489 (m) cc_final: 0.7208 (p) REVERT: A 1029 PHE cc_start: 0.6492 (OUTLIER) cc_final: 0.5500 (m-80) outliers start: 26 outliers final: 14 residues processed: 206 average time/residue: 1.3931 time to fit residues: 305.7649 Evaluate side-chains 204 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 186 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 399 ARG Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 539 LYS Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1029 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 54 optimal weight: 0.3980 chunk 10 optimal weight: 0.5980 chunk 87 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.0980 chunk 96 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 GLN A 959 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9663 Z= 0.210 Angle : 0.534 9.197 13219 Z= 0.284 Chirality : 0.040 0.171 1501 Planarity : 0.004 0.055 1638 Dihedral : 14.956 137.710 1522 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.64 % Allowed : 19.73 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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: 0.97 (0.25), residues: 1135 helix: 1.60 (0.21), residues: 641 sheet: -0.51 (0.54), residues: 96 loop : -0.56 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 35 HIS 0.004 0.001 HIS A 260 PHE 0.015 0.001 PHE A 779 TYR 0.027 0.002 TYR A 445 ARG 0.013 0.000 ARG A 758 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 188 time to evaluate : 1.027 Fit side-chains revert: symmetry clash REVERT: A 94 ILE cc_start: 0.7495 (pt) cc_final: 0.7213 (pp) REVERT: A 151 ASP cc_start: 0.6863 (t70) cc_final: 0.6509 (t0) REVERT: A 235 LYS cc_start: 0.7014 (OUTLIER) cc_final: 0.6704 (tppt) REVERT: A 264 ASP cc_start: 0.7015 (p0) cc_final: 0.6739 (p0) REVERT: A 266 TRP cc_start: 0.6618 (t-100) cc_final: 0.6192 (t-100) REVERT: A 312 ARG cc_start: 0.7241 (mpp80) cc_final: 0.6968 (mtm-85) REVERT: A 322 ASN cc_start: 0.7166 (t0) cc_final: 0.6914 (t0) REVERT: A 483 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8589 (mt) REVERT: A 544 LYS cc_start: 0.7848 (mttp) cc_final: 0.7619 (mttp) REVERT: A 740 MET cc_start: 0.8084 (mmm) cc_final: 0.7531 (mmm) REVERT: A 819 ASP cc_start: 0.6876 (t70) cc_final: 0.6655 (t0) REVERT: A 831 GLN cc_start: 0.7244 (tp-100) cc_final: 0.6976 (mm-40) REVERT: A 989 ASN cc_start: 0.7699 (OUTLIER) cc_final: 0.7469 (t0) REVERT: A 1018 SER cc_start: 0.7497 (m) cc_final: 0.7220 (p) REVERT: A 1029 PHE cc_start: 0.6522 (OUTLIER) cc_final: 0.5443 (m-80) outliers start: 25 outliers final: 17 residues processed: 201 average time/residue: 1.4127 time to fit residues: 302.5059 Evaluate side-chains 203 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 182 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 399 ARG Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 959 GLN Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1133 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.5980 chunk 106 optimal weight: 0.4980 chunk 62 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 97 optimal weight: 0.0870 chunk 102 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 109 optimal weight: 0.0770 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9663 Z= 0.189 Angle : 0.535 9.470 13219 Z= 0.284 Chirality : 0.039 0.182 1501 Planarity : 0.005 0.057 1638 Dihedral : 14.938 138.776 1522 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.53 % Allowed : 20.57 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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: 1.03 (0.25), residues: 1135 helix: 1.62 (0.21), residues: 641 sheet: -0.40 (0.54), residues: 96 loop : -0.54 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 35 HIS 0.003 0.001 HIS A 116 PHE 0.016 0.001 PHE A 779 TYR 0.012 0.002 TYR A 217 ARG 0.014 0.000 ARG A 758 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 186 time to evaluate : 1.055 Fit side-chains revert: symmetry clash REVERT: A 94 ILE cc_start: 0.7483 (pt) cc_final: 0.7194 (pp) REVERT: A 151 ASP cc_start: 0.6883 (t70) cc_final: 0.6523 (t0) REVERT: A 235 LYS cc_start: 0.6987 (OUTLIER) cc_final: 0.6669 (tppt) REVERT: A 264 ASP cc_start: 0.6949 (p0) cc_final: 0.6699 (p0) REVERT: A 266 TRP cc_start: 0.6504 (t-100) cc_final: 0.6054 (t-100) REVERT: A 312 ARG cc_start: 0.7214 (mpp80) cc_final: 0.6943 (mtm-85) REVERT: A 322 ASN cc_start: 0.7193 (t0) cc_final: 0.6921 (t0) REVERT: A 483 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8580 (mt) REVERT: A 544 LYS cc_start: 0.7829 (mttp) cc_final: 0.7610 (mttp) REVERT: A 692 VAL cc_start: 0.7799 (t) cc_final: 0.7576 (t) REVERT: A 740 MET cc_start: 0.8072 (mmm) cc_final: 0.7491 (mmm) REVERT: A 794 GLN cc_start: 0.7349 (tt0) cc_final: 0.7120 (tt0) REVERT: A 819 ASP cc_start: 0.6864 (t70) cc_final: 0.6640 (t0) REVERT: A 831 GLN cc_start: 0.7249 (tp-100) cc_final: 0.6978 (mm-40) REVERT: A 989 ASN cc_start: 0.7676 (OUTLIER) cc_final: 0.7448 (t0) REVERT: A 1018 SER cc_start: 0.7462 (m) cc_final: 0.7181 (p) REVERT: A 1029 PHE cc_start: 0.6412 (OUTLIER) cc_final: 0.5341 (m-80) outliers start: 24 outliers final: 16 residues processed: 198 average time/residue: 1.4294 time to fit residues: 301.9443 Evaluate side-chains 203 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 183 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1133 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 1.9990 chunk 51 optimal weight: 0.1980 chunk 75 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 91 optimal weight: 0.0870 chunk 9 optimal weight: 1.9990 chunk 70 optimal weight: 0.0040 chunk 55 optimal weight: 0.7980 chunk 72 optimal weight: 0.1980 chunk 97 optimal weight: 0.6980 overall best weight: 0.2170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9663 Z= 0.162 Angle : 0.527 10.099 13219 Z= 0.279 Chirality : 0.038 0.158 1501 Planarity : 0.004 0.059 1638 Dihedral : 14.902 140.403 1522 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.74 % Allowed : 20.68 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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: 1.17 (0.25), residues: 1135 helix: 1.71 (0.21), residues: 642 sheet: -0.07 (0.55), residues: 94 loop : -0.51 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 35 HIS 0.002 0.001 HIS A 260 PHE 0.014 0.001 PHE A 779 TYR 0.029 0.002 TYR A 445 ARG 0.013 0.000 ARG A 758 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 187 time to evaluate : 1.086 Fit side-chains revert: symmetry clash REVERT: A 94 ILE cc_start: 0.7458 (pt) cc_final: 0.7154 (pp) REVERT: A 151 ASP cc_start: 0.6876 (t70) cc_final: 0.6537 (t0) REVERT: A 211 MET cc_start: 0.6121 (OUTLIER) cc_final: 0.5894 (mmm) REVERT: A 264 ASP cc_start: 0.6901 (p0) cc_final: 0.6676 (p0) REVERT: A 312 ARG cc_start: 0.7180 (mpp80) cc_final: 0.6892 (mtm-85) REVERT: A 322 ASN cc_start: 0.7197 (t0) cc_final: 0.6934 (t0) REVERT: A 548 LYS cc_start: 0.7833 (mtpt) cc_final: 0.7612 (mtmt) REVERT: A 692 VAL cc_start: 0.7753 (t) cc_final: 0.7525 (t) REVERT: A 740 MET cc_start: 0.8069 (mmm) cc_final: 0.7438 (mmm) REVERT: A 794 GLN cc_start: 0.7263 (tt0) cc_final: 0.6998 (tt0) REVERT: A 819 ASP cc_start: 0.6827 (t70) cc_final: 0.6610 (t0) REVERT: A 831 GLN cc_start: 0.7259 (tp-100) cc_final: 0.6983 (mm-40) REVERT: A 1029 PHE cc_start: 0.6290 (OUTLIER) cc_final: 0.5320 (m-80) REVERT: A 1162 MET cc_start: 0.6174 (OUTLIER) cc_final: 0.5649 (tpt) outliers start: 26 outliers final: 15 residues processed: 200 average time/residue: 1.3209 time to fit residues: 281.9575 Evaluate side-chains 195 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 177 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1162 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 91 optimal weight: 0.0970 chunk 38 optimal weight: 0.5980 chunk 93 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 5 optimal weight: 0.0980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 ASN A 772 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.161221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.144742 restraints weight = 12299.637| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 1.64 r_work: 0.3762 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9663 Z= 0.213 Angle : 0.561 11.466 13219 Z= 0.294 Chirality : 0.040 0.184 1501 Planarity : 0.005 0.059 1638 Dihedral : 14.928 141.073 1522 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.22 % Allowed : 21.73 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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: 1.09 (0.25), residues: 1135 helix: 1.67 (0.21), residues: 639 sheet: -0.33 (0.54), residues: 96 loop : -0.50 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 35 HIS 0.003 0.001 HIS A 260 PHE 0.013 0.001 PHE A 779 TYR 0.013 0.002 TYR A 874 ARG 0.015 0.000 ARG A 758 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4810.46 seconds wall clock time: 86 minutes 24.97 seconds (5184.97 seconds total)