Starting phenix.real_space_refine on Fri Dec 8 00:33:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e29_27829/12_2023/8e29_27829.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e29_27829/12_2023/8e29_27829.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e29_27829/12_2023/8e29_27829.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e29_27829/12_2023/8e29_27829.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e29_27829/12_2023/8e29_27829.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e29_27829/12_2023/8e29_27829.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.018 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 33 5.49 5 S 31 5.16 5 C 3821 2.51 5 N 1053 2.21 5 O 1259 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 91": "OD1" <-> "OD2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "A PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A GLU 332": "OE1" <-> "OE2" Residue "A GLU 339": "OE1" <-> "OE2" Residue "A TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 367": "OE1" <-> "OE2" Residue "A ASP 383": "OD1" <-> "OD2" Residue "A ASP 389": "OD1" <-> "OD2" Residue "A PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 419": "OE1" <-> "OE2" Residue "A ASP 424": "OD1" <-> "OD2" Residue "A TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 460": "OD1" <-> "OD2" Residue "A GLU 473": "OE1" <-> "OE2" Residue "A PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 495": "OE1" <-> "OE2" Residue "A GLU 524": "OE1" <-> "OE2" Residue "A PHE 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 546": "OD1" <-> "OD2" Residue "A PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 584": "OE1" <-> "OE2" Residue "A PHE 585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 633": "OD1" <-> "OD2" Residue "A TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 708": "OD1" <-> "OD2" Residue "A GLU 751": "OE1" <-> "OE2" Residue "A PHE 757": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 764": "OE1" <-> "OE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 796": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 841": "OE1" <-> "OE2" Residue "A GLU 847": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 6197 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 692, 5511 Classifications: {'peptide': 692} Link IDs: {'PTRANS': 41, 'TRANS': 650} Chain breaks: 2 Chain: "B" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 686 Classifications: {'RNA': 33} Modifications used: {'rna2p_pyr': 6, 'rna3p_pur': 9, 'rna3p_pyr': 18} Link IDs: {'rna2p': 5, 'rna3p': 27} Time building chain proxies: 4.13, per 1000 atoms: 0.67 Number of scatterers: 6197 At special positions: 0 Unit cell: (77.05, 87.1, 105.19, 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 31 16.00 P 33 15.00 O 1259 8.00 N 1053 7.00 C 3821 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.44 Conformation dependent library (CDL) restraints added in 1.2 seconds 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1322 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 9 sheets defined 30.8% alpha, 23.6% beta 8 base pairs and 17 stacking pairs defined. Time for finding SS restraints: 2.14 Creating SS restraints... Processing helix chain 'A' and resid 55 through 66 Processing helix chain 'A' and resid 329 through 341 Processing helix chain 'A' and resid 348 through 353 Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.734A pdb=" N PHE A 368 " --> pdb=" O PRO A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 430 removed outlier: 3.538A pdb=" N ARG A 430 " --> pdb=" O VAL A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 451 Processing helix chain 'A' and resid 495 through 502 Processing helix chain 'A' and resid 509 through 513 removed outlier: 3.645A pdb=" N GLU A 512 " --> pdb=" O PRO A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 547 removed outlier: 3.795A pdb=" N VAL A 525 " --> pdb=" O SER A 521 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLN A 538 " --> pdb=" O GLY A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 601 removed outlier: 3.759A pdb=" N VAL A 582 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU A 583 " --> pdb=" O ASN A 579 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 627 removed outlier: 3.709A pdb=" N ASP A 620 " --> pdb=" O ARG A 616 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLN A 627 " --> pdb=" O GLU A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 649 removed outlier: 4.166A pdb=" N PHE A 648 " --> pdb=" O LEU A 644 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY A 649 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 666 Processing helix chain 'A' and resid 706 through 719 Processing helix chain 'A' and resid 728 through 765 removed outlier: 3.586A pdb=" N LEU A 732 " --> pdb=" O ALA A 728 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN A 733 " --> pdb=" O PRO A 729 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 72 removed outlier: 7.096A pdb=" N LEU A 110 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LYS A 114 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N VAL A 235 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ASP A 97 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N VAL A 235 " --> pdb=" O ASP A 97 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 246 through 252 removed outlier: 6.791A pdb=" N LEU A 319 " --> pdb=" O PRO A 281 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N LEU A 316 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE A 302 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N SER A 322 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LEU A 300 " --> pdb=" O SER A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 372 through 373 removed outlier: 3.822A pdb=" N ASP A 478 " --> pdb=" O THR A 469 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 380 through 382 removed outlier: 6.365A pdb=" N THR A 381 " --> pdb=" O LEU A 492 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 434 through 435 Processing sheet with id=AA6, first strand: chain 'A' and resid 556 through 560 removed outlier: 6.459A pdb=" N ALA A 557 " --> pdb=" O CYS A 570 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N CYS A 570 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR A 559 " --> pdb=" O GLN A 568 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 606 through 609 Processing sheet with id=AA8, first strand: chain 'A' and resid 792 through 796 removed outlier: 7.095A pdb=" N ALA A 781 " --> pdb=" O ILE A 777 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ILE A 777 " --> pdb=" O ALA A 781 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ASP A 783 " --> pdb=" O MET A 775 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 802 through 810 235 hydrogen bonds defined for protein. 669 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 23 hydrogen bonds 46 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 17 stacking parallelities Total time for adding SS restraints: 2.12 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1300 1.33 - 1.45: 1510 1.45 - 1.57: 3468 1.57 - 1.69: 65 1.69 - 1.81: 47 Bond restraints: 6390 Sorted by residual: bond pdb=" CG LEU A 691 " pdb=" CD1 LEU A 691 " ideal model delta sigma weight residual 1.521 1.428 0.093 3.30e-02 9.18e+02 7.91e+00 bond pdb=" CG LEU A 691 " pdb=" CD2 LEU A 691 " ideal model delta sigma weight residual 1.521 1.429 0.092 3.30e-02 9.18e+02 7.77e+00 bond pdb=" CB TRP A 468 " pdb=" CG TRP A 468 " ideal model delta sigma weight residual 1.498 1.424 0.074 3.10e-02 1.04e+03 5.69e+00 bond pdb=" CA SER A 465 " pdb=" CB SER A 465 " ideal model delta sigma weight residual 1.536 1.476 0.060 2.53e-02 1.56e+03 5.60e+00 bond pdb=" CG LEU A 455 " pdb=" CD2 LEU A 455 " ideal model delta sigma weight residual 1.521 1.449 0.072 3.30e-02 9.18e+02 4.71e+00 ... (remaining 6385 not shown) Histogram of bond angle deviations from ideal: 99.45 - 106.38: 387 106.38 - 113.31: 3409 113.31 - 120.23: 2524 120.23 - 127.16: 2366 127.16 - 134.09: 112 Bond angle restraints: 8798 Sorted by residual: angle pdb=" N ARG A 104 " pdb=" CA ARG A 104 " pdb=" CB ARG A 104 " ideal model delta sigma weight residual 111.84 106.31 5.53 1.49e+00 4.50e-01 1.38e+01 angle pdb=" N HIS A 688 " pdb=" CA HIS A 688 " pdb=" C HIS A 688 " ideal model delta sigma weight residual 109.46 103.34 6.12 1.66e+00 3.63e-01 1.36e+01 angle pdb=" CA GLU A 512 " pdb=" CB GLU A 512 " pdb=" CG GLU A 512 " ideal model delta sigma weight residual 114.10 121.40 -7.30 2.00e+00 2.50e-01 1.33e+01 angle pdb=" C CYS A 449 " pdb=" N GLU A 450 " pdb=" CA GLU A 450 " ideal model delta sigma weight residual 122.60 117.02 5.58 1.56e+00 4.11e-01 1.28e+01 angle pdb=" N SER A 701 " pdb=" CA SER A 701 " pdb=" C SER A 701 " ideal model delta sigma weight residual 109.81 117.59 -7.78 2.21e+00 2.05e-01 1.24e+01 ... (remaining 8793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.48: 3540 21.48 - 42.96: 294 42.96 - 64.43: 79 64.43 - 85.91: 18 85.91 - 107.39: 2 Dihedral angle restraints: 3933 sinusoidal: 1903 harmonic: 2030 Sorted by residual: dihedral pdb=" O4' U B 30 " pdb=" C1' U B 30 " pdb=" N1 U B 30 " pdb=" C2 U B 30 " ideal model delta sinusoidal sigma weight residual -160.00 -105.96 -54.04 1 1.50e+01 4.44e-03 1.76e+01 dihedral pdb=" CA ARG A 277 " pdb=" C ARG A 277 " pdb=" N ILE A 278 " pdb=" CA ILE A 278 " ideal model delta harmonic sigma weight residual -180.00 -159.56 -20.44 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA MET A 617 " pdb=" C MET A 617 " pdb=" N LEU A 618 " pdb=" CA LEU A 618 " ideal model delta harmonic sigma weight residual 180.00 160.52 19.48 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 3930 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 672 0.060 - 0.119: 248 0.119 - 0.179: 86 0.179 - 0.238: 11 0.238 - 0.298: 3 Chirality restraints: 1020 Sorted by residual: chirality pdb=" CB VAL A 113 " pdb=" CA VAL A 113 " pdb=" CG1 VAL A 113 " pdb=" CG2 VAL A 113 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CG LEU A 560 " pdb=" CB LEU A 560 " pdb=" CD1 LEU A 560 " pdb=" CD2 LEU A 560 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA ILE A 75 " pdb=" N ILE A 75 " pdb=" C ILE A 75 " pdb=" CB ILE A 75 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 1017 not shown) Planarity restraints: 1019 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 708 " 0.025 2.00e-02 2.50e+03 5.08e-02 2.58e+01 pdb=" CG ASP A 708 " -0.088 2.00e-02 2.50e+03 pdb=" OD1 ASP A 708 " 0.030 2.00e-02 2.50e+03 pdb=" OD2 ASP A 708 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 743 " 0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C ARG A 743 " -0.059 2.00e-02 2.50e+03 pdb=" O ARG A 743 " 0.022 2.00e-02 2.50e+03 pdb=" N MET A 744 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 583 " -0.017 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C GLU A 583 " 0.057 2.00e-02 2.50e+03 pdb=" O GLU A 583 " -0.021 2.00e-02 2.50e+03 pdb=" N GLU A 584 " -0.019 2.00e-02 2.50e+03 ... (remaining 1016 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 1796 2.82 - 3.34: 4911 3.34 - 3.86: 9644 3.86 - 4.38: 10585 4.38 - 4.90: 19143 Nonbonded interactions: 46079 Sorted by model distance: nonbonded pdb=" OH TYR A 575 " pdb=" OE1 GLU A 583 " model vdw 2.305 2.440 nonbonded pdb=" O THR A 835 " pdb=" OG SER A 838 " model vdw 2.310 2.440 nonbonded pdb=" OH TYR A 653 " pdb=" O PHE A 837 " model vdw 2.311 2.440 nonbonded pdb=" O THR A 386 " pdb=" OG1 THR A 386 " model vdw 2.329 2.440 nonbonded pdb=" NH1 ARG A 388 " pdb=" OE2 GLU A 450 " model vdw 2.372 2.520 ... (remaining 46074 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: 1.450 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: 5.940 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 22.510 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 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 : 0.012 0.101 6390 Z= 0.809 Angle : 1.137 9.374 8798 Z= 0.630 Chirality : 0.069 0.298 1020 Planarity : 0.008 0.058 1019 Dihedral : 17.037 107.388 2611 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.66 % Allowed : 6.90 % Favored : 92.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.29), residues: 686 helix: -1.02 (0.32), residues: 205 sheet: 0.18 (0.41), residues: 155 loop : -1.61 (0.30), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.005 TRP A 468 HIS 0.017 0.002 HIS A 526 PHE 0.049 0.004 PHE A 699 TYR 0.028 0.005 TYR A 853 ARG 0.010 0.001 ARG A 104 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 70 time to evaluate : 0.727 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 73 average time/residue: 0.2143 time to fit residues: 20.8477 Evaluate side-chains 56 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.677 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0717 time to fit residues: 1.2005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 30 optimal weight: 0.0770 chunk 18 optimal weight: 0.0970 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.5536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6390 Z= 0.170 Angle : 0.573 8.148 8798 Z= 0.292 Chirality : 0.040 0.139 1020 Planarity : 0.005 0.039 1019 Dihedral : 15.750 108.258 1224 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.82 % Allowed : 11.49 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.31), residues: 686 helix: 0.68 (0.37), residues: 214 sheet: 0.34 (0.40), residues: 168 loop : -1.49 (0.32), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 468 HIS 0.003 0.001 HIS A 526 PHE 0.016 0.001 PHE A 699 TYR 0.010 0.001 TYR A 674 ARG 0.004 0.000 ARG A 803 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 63 time to evaluate : 0.680 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 66 average time/residue: 0.2070 time to fit residues: 18.3528 Evaluate side-chains 56 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 0.635 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0619 time to fit residues: 1.0236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 70 optimal weight: 30.0000 chunk 58 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 562 HIS A 831 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6390 Z= 0.285 Angle : 0.586 6.948 8798 Z= 0.299 Chirality : 0.041 0.150 1020 Planarity : 0.005 0.042 1019 Dihedral : 15.752 108.723 1224 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.99 % Allowed : 14.29 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.32), residues: 686 helix: 0.84 (0.37), residues: 214 sheet: 0.46 (0.40), residues: 172 loop : -1.49 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 468 HIS 0.007 0.001 HIS A 526 PHE 0.017 0.002 PHE A 699 TYR 0.013 0.002 TYR A 674 ARG 0.004 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.766 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 61 average time/residue: 0.2059 time to fit residues: 17.1690 Evaluate side-chains 60 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.670 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0600 time to fit residues: 1.5016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 33 optimal weight: 0.0570 chunk 7 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 69 optimal weight: 30.0000 chunk 34 optimal weight: 10.0000 chunk 62 optimal weight: 0.6980 chunk 18 optimal weight: 0.0870 overall best weight: 0.9680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6390 Z= 0.178 Angle : 0.511 6.705 8798 Z= 0.260 Chirality : 0.039 0.143 1020 Planarity : 0.004 0.037 1019 Dihedral : 15.665 106.967 1224 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.49 % Allowed : 15.11 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.32), residues: 686 helix: 1.26 (0.37), residues: 213 sheet: 0.56 (0.41), residues: 172 loop : -1.42 (0.33), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 468 HIS 0.004 0.001 HIS A 526 PHE 0.011 0.001 PHE A 699 TYR 0.010 0.001 TYR A 674 ARG 0.004 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 63 time to evaluate : 0.701 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 66 average time/residue: 0.2051 time to fit residues: 18.3902 Evaluate side-chains 60 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.674 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0910 time to fit residues: 1.0967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 62 optimal weight: 0.3980 chunk 17 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 831 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6390 Z= 0.145 Angle : 0.483 6.561 8798 Z= 0.245 Chirality : 0.038 0.140 1020 Planarity : 0.004 0.035 1019 Dihedral : 15.567 104.511 1224 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.99 % Allowed : 15.76 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.33), residues: 686 helix: 1.62 (0.38), residues: 209 sheet: 0.69 (0.41), residues: 170 loop : -1.22 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 468 HIS 0.003 0.000 HIS A 526 PHE 0.009 0.001 PHE A 481 TYR 0.009 0.001 TYR A 674 ARG 0.005 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 65 time to evaluate : 0.692 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 68 average time/residue: 0.1969 time to fit residues: 18.0910 Evaluate side-chains 61 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 57 time to evaluate : 0.533 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0511 time to fit residues: 1.1841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 69 optimal weight: 30.0000 chunk 57 optimal weight: 0.7980 chunk 32 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 831 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6390 Z= 0.224 Angle : 0.528 6.108 8798 Z= 0.268 Chirality : 0.039 0.148 1020 Planarity : 0.004 0.036 1019 Dihedral : 15.573 102.162 1224 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.99 % Allowed : 16.91 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.33), residues: 686 helix: 1.44 (0.38), residues: 213 sheet: 0.71 (0.41), residues: 170 loop : -1.23 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 468 HIS 0.005 0.001 HIS A 526 PHE 0.013 0.001 PHE A 464 TYR 0.011 0.001 TYR A 340 ARG 0.005 0.000 ARG A 794 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.710 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 60 average time/residue: 0.1896 time to fit residues: 15.8500 Evaluate side-chains 56 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 0.699 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0607 time to fit residues: 1.0050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 50 optimal weight: 0.0020 chunk 58 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 30.0000 chunk 43 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 27 optimal weight: 0.2980 chunk 41 optimal weight: 0.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 831 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6390 Z= 0.134 Angle : 0.472 6.248 8798 Z= 0.239 Chirality : 0.037 0.139 1020 Planarity : 0.004 0.033 1019 Dihedral : 15.475 99.742 1224 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.15 % Allowed : 17.41 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.33), residues: 686 helix: 1.62 (0.38), residues: 215 sheet: 0.78 (0.41), residues: 170 loop : -1.19 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 468 HIS 0.002 0.001 HIS A 526 PHE 0.009 0.001 PHE A 464 TYR 0.008 0.001 TYR A 674 ARG 0.004 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 61 time to evaluate : 0.685 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 65 average time/residue: 0.1940 time to fit residues: 17.2182 Evaluate side-chains 62 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 58 time to evaluate : 0.683 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0787 time to fit residues: 1.4764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 66 optimal weight: 0.0470 chunk 60 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 831 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6390 Z= 0.168 Angle : 0.489 6.727 8798 Z= 0.247 Chirality : 0.038 0.146 1020 Planarity : 0.004 0.034 1019 Dihedral : 15.453 97.586 1224 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.33 % Allowed : 18.39 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.33), residues: 686 helix: 1.62 (0.38), residues: 215 sheet: 0.83 (0.42), residues: 170 loop : -1.18 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 468 HIS 0.003 0.001 HIS A 526 PHE 0.010 0.001 PHE A 481 TYR 0.009 0.001 TYR A 674 ARG 0.004 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 0.622 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 58 average time/residue: 0.1899 time to fit residues: 15.1359 Evaluate side-chains 56 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.574 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 0.0070 chunk 58 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 68 optimal weight: 0.0770 chunk 41 optimal weight: 1.9990 overall best weight: 0.5756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 831 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6390 Z= 0.138 Angle : 0.472 7.094 8798 Z= 0.238 Chirality : 0.037 0.142 1020 Planarity : 0.004 0.035 1019 Dihedral : 15.392 94.631 1224 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.16 % Allowed : 18.72 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.34), residues: 686 helix: 1.69 (0.38), residues: 216 sheet: 0.90 (0.42), residues: 170 loop : -1.13 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 468 HIS 0.002 0.000 HIS A 526 PHE 0.009 0.001 PHE A 481 TYR 0.008 0.001 TYR A 674 ARG 0.005 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 0.685 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 55 average time/residue: 0.1892 time to fit residues: 14.4871 Evaluate side-chains 56 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 0.725 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0847 time to fit residues: 1.1249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 831 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6390 Z= 0.275 Angle : 0.546 7.203 8798 Z= 0.276 Chirality : 0.040 0.151 1020 Planarity : 0.004 0.036 1019 Dihedral : 15.441 92.473 1224 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.66 % Allowed : 18.56 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.33), residues: 686 helix: 1.31 (0.37), residues: 220 sheet: 0.89 (0.42), residues: 170 loop : -1.30 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 468 HIS 0.006 0.001 HIS A 526 PHE 0.015 0.002 PHE A 481 TYR 0.011 0.001 TYR A 674 ARG 0.005 0.000 ARG A 102 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.692 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 56 average time/residue: 0.2052 time to fit residues: 15.8037 Evaluate side-chains 56 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 time to evaluate : 0.672 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0703 time to fit residues: 1.2703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 0.0570 chunk 8 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 57 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 831 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.177905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.120504 restraints weight = 6554.522| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 3.13 r_work: 0.3315 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6390 Z= 0.141 Angle : 0.478 7.224 8798 Z= 0.242 Chirality : 0.038 0.143 1020 Planarity : 0.004 0.036 1019 Dihedral : 15.338 89.802 1224 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 18.72 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.33), residues: 686 helix: 1.65 (0.38), residues: 216 sheet: 0.88 (0.42), residues: 171 loop : -1.22 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 468 HIS 0.002 0.000 HIS A 526 PHE 0.009 0.001 PHE A 481 TYR 0.008 0.001 TYR A 674 ARG 0.004 0.000 ARG A 794 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1624.91 seconds wall clock time: 29 minutes 51.93 seconds (1791.93 seconds total)