Starting phenix.real_space_refine on Tue Feb 13 12:36:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e29_27829/02_2024/8e29_27829.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e29_27829/02_2024/8e29_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_27829/02_2024/8e29_27829.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e29_27829/02_2024/8e29_27829.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e29_27829/02_2024/8e29_27829.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e29_27829/02_2024/8e29_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-dev-5238/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: 4.24, per 1000 atoms: 0.68 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: 2.45 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: 2.16 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: 2.19 Time building geometry restraints manager: 2.66 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: 3567 21.48 - 42.96: 310 42.96 - 64.43: 100 64.43 - 85.91: 18 85.91 - 107.39: 2 Dihedral angle restraints: 3997 sinusoidal: 1967 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 3994 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: 1.140 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: 6.050 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.140 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.490 ------------------------------------------------------------------------------- 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 : 17.732 107.388 2675 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 : 0.695 Fit side-chains REVERT: A 424 ASP cc_start: 0.8112 (t70) cc_final: 0.7877 (t0) REVERT: A 726 ASP cc_start: 0.7801 (p0) cc_final: 0.7515 (t0) REVERT: A 851 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7078 (mp) outliers start: 4 outliers final: 2 residues processed: 73 average time/residue: 0.2010 time to fit residues: 19.3052 Evaluate side-chains 57 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 775 MET Chi-restraints excluded: chain A residue 851 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 1.9990 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: 0.7443 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6390 Z= 0.165 Angle : 0.568 7.878 8798 Z= 0.289 Chirality : 0.040 0.139 1020 Planarity : 0.005 0.040 1019 Dihedral : 17.488 108.221 1295 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.99 % Allowed : 11.66 % Favored : 87.36 % 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: -0.53 (0.31), residues: 686 helix: 0.63 (0.36), residues: 214 sheet: 0.34 (0.40), residues: 168 loop : -1.48 (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 0.014 0.001 PHE A 699 TYR 0.011 0.001 TYR A 674 ARG 0.003 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 69 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 0.959 Fit side-chains REVERT: A 424 ASP cc_start: 0.8195 (t70) cc_final: 0.7989 (t0) REVERT: A 726 ASP cc_start: 0.7769 (p0) cc_final: 0.7506 (t0) REVERT: A 803 ARG cc_start: 0.7741 (ttp80) cc_final: 0.7469 (ttp-110) REVERT: A 851 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.6987 (mp) outliers start: 6 outliers final: 1 residues processed: 68 average time/residue: 0.2146 time to fit residues: 20.3443 Evaluate side-chains 60 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 857 LEU 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: 4.9990 chunk 18 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 30.0000 chunk 58 optimal weight: 0.8980 chunk 64 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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: 0.7543 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6390 Z= 0.299 Angle : 0.597 7.068 8798 Z= 0.304 Chirality : 0.041 0.155 1020 Planarity : 0.005 0.042 1019 Dihedral : 17.394 108.739 1290 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.15 % Allowed : 14.29 % Favored : 84.56 % 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: -0.39 (0.32), residues: 686 helix: 0.81 (0.37), residues: 214 sheet: 0.45 (0.40), residues: 172 loop : -1.48 (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 340 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 63 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.642 Fit side-chains REVERT: A 726 ASP cc_start: 0.7747 (p0) cc_final: 0.7518 (t0) REVERT: A 803 ARG cc_start: 0.7743 (ttp80) cc_final: 0.7515 (ttp-110) REVERT: A 851 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.6905 (mp) outliers start: 7 outliers final: 5 residues processed: 62 average time/residue: 0.1959 time to fit residues: 16.2411 Evaluate side-chains 59 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 53 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 857 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 69 optimal weight: 30.0000 chunk 34 optimal weight: 9.9990 chunk 62 optimal weight: 0.6980 chunk 18 optimal weight: 0.0770 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 831 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.1774 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= 0.143 Angle : 0.495 6.973 8798 Z= 0.251 Chirality : 0.038 0.140 1020 Planarity : 0.004 0.037 1019 Dihedral : 17.215 106.942 1290 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 1.64 % Allowed : 14.78 % Favored : 83.58 % 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: 0.05 (0.32), residues: 686 helix: 1.46 (0.38), residues: 209 sheet: 0.53 (0.40), residues: 172 loop : -1.31 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 468 HIS 0.002 0.001 HIS A 598 PHE 0.010 0.001 PHE A 699 TYR 0.009 0.001 TYR A 674 ARG 0.005 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 74 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 64 time to evaluate : 0.638 Fit side-chains REVERT: A 58 ASP cc_start: 0.8241 (t70) cc_final: 0.8029 (t0) REVERT: A 726 ASP cc_start: 0.7721 (p0) cc_final: 0.7519 (t0) REVERT: A 794 ARG cc_start: 0.8374 (ttm-80) cc_final: 0.8114 (tpp-160) REVERT: A 851 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.6843 (mp) outliers start: 10 outliers final: 5 residues processed: 72 average time/residue: 0.1904 time to fit residues: 18.4611 Evaluate side-chains 65 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 856 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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: 0.7502 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6390 Z= 0.219 Angle : 0.523 6.501 8798 Z= 0.265 Chirality : 0.039 0.147 1020 Planarity : 0.004 0.037 1019 Dihedral : 17.191 105.011 1290 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.48 % Allowed : 16.42 % 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: 0.04 (0.33), residues: 686 helix: 1.41 (0.37), residues: 212 sheet: 0.58 (0.40), residues: 172 loop : -1.34 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 468 HIS 0.005 0.001 HIS A 526 PHE 0.013 0.001 PHE A 699 TYR 0.011 0.001 TYR A 340 ARG 0.004 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 69 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 60 time to evaluate : 0.667 Fit side-chains REVERT: A 58 ASP cc_start: 0.8252 (t70) cc_final: 0.8024 (t0) REVERT: A 726 ASP cc_start: 0.7728 (p0) cc_final: 0.7507 (t0) REVERT: A 803 ARG cc_start: 0.7492 (ttp-110) cc_final: 0.7271 (ttp-110) REVERT: A 851 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.6844 (mp) outliers start: 9 outliers final: 5 residues processed: 66 average time/residue: 0.1957 time to fit residues: 17.4392 Evaluate side-chains 64 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 857 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 0.2980 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 69 optimal weight: 30.0000 chunk 57 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- 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: 0.7546 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6390 Z= 0.289 Angle : 0.562 6.796 8798 Z= 0.285 Chirality : 0.041 0.152 1020 Planarity : 0.004 0.038 1019 Dihedral : 17.131 102.570 1290 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.63 % Allowed : 16.26 % 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: -0.09 (0.33), residues: 686 helix: 1.26 (0.38), residues: 212 sheet: 0.56 (0.41), residues: 172 loop : -1.42 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 468 HIS 0.007 0.001 HIS A 526 PHE 0.014 0.002 PHE A 782 TYR 0.012 0.002 TYR A 340 ARG 0.006 0.000 ARG A 102 *********************** 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 72 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 56 time to evaluate : 0.741 Fit side-chains REVERT: A 657 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.6451 (mtt90) REVERT: A 726 ASP cc_start: 0.7764 (p0) cc_final: 0.7536 (t0) REVERT: A 851 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7066 (mp) outliers start: 16 outliers final: 10 residues processed: 68 average time/residue: 0.1884 time to fit residues: 17.3199 Evaluate side-chains 67 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 55 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 857 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 30.0000 chunk 43 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 27 optimal weight: 0.0040 chunk 41 optimal weight: 1.9990 overall best weight: 0.9996 ------------------------------------------------------------------------------- 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: 0.7497 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6390 Z= 0.185 Angle : 0.506 6.244 8798 Z= 0.258 Chirality : 0.038 0.144 1020 Planarity : 0.004 0.037 1019 Dihedral : 16.963 100.729 1290 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.30 % Allowed : 16.75 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.33), residues: 686 helix: 1.48 (0.38), residues: 213 sheet: 0.71 (0.42), residues: 170 loop : -1.26 (0.35), residues: 303 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 0.010 0.001 PHE A 782 TYR 0.009 0.001 TYR A 674 ARG 0.004 0.000 ARG A 102 *********************** 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 73 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 59 time to evaluate : 0.692 Fit side-chains REVERT: A 657 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.6385 (mtt90) REVERT: A 726 ASP cc_start: 0.7763 (p0) cc_final: 0.7539 (t0) REVERT: A 851 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.6865 (mp) outliers start: 14 outliers final: 9 residues processed: 69 average time/residue: 0.1980 time to fit residues: 18.7555 Evaluate side-chains 70 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 59 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 857 LEU 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: 2.9990 chunk 44 optimal weight: 0.0970 chunk 47 optimal weight: 1.9990 chunk 34 optimal weight: 0.0970 chunk 6 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 63 optimal weight: 0.0050 chunk 66 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 overall best weight: 0.3990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6390 Z= 0.126 Angle : 0.460 6.333 8798 Z= 0.234 Chirality : 0.037 0.136 1020 Planarity : 0.004 0.037 1019 Dihedral : 16.731 97.213 1290 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.31 % Allowed : 18.06 % Favored : 80.62 % 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 (0.34), residues: 686 helix: 1.72 (0.38), residues: 215 sheet: 0.78 (0.42), residues: 170 loop : -1.19 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 468 HIS 0.002 0.001 HIS A 610 PHE 0.007 0.001 PHE A 481 TYR 0.007 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 72 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 0.656 Fit side-chains REVERT: A 726 ASP cc_start: 0.7746 (p0) cc_final: 0.7516 (t0) REVERT: A 803 ARG cc_start: 0.7310 (ttp-110) cc_final: 0.7027 (ttp-110) outliers start: 8 outliers final: 5 residues processed: 68 average time/residue: 0.1621 time to fit residues: 15.5964 Evaluate side-chains 62 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 856 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.7456 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6390 Z= 0.167 Angle : 0.494 6.828 8798 Z= 0.250 Chirality : 0.038 0.146 1020 Planarity : 0.004 0.035 1019 Dihedral : 16.640 94.976 1288 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.48 % Allowed : 18.88 % Favored : 79.64 % 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 (0.34), residues: 686 helix: 1.90 (0.38), residues: 209 sheet: 0.86 (0.42), residues: 170 loop : -1.10 (0.35), residues: 307 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 340 ARG 0.004 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 65 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 56 time to evaluate : 0.703 Fit side-chains REVERT: A 726 ASP cc_start: 0.7754 (p0) cc_final: 0.7491 (t0) outliers start: 9 outliers final: 8 residues processed: 62 average time/residue: 0.1929 time to fit residues: 16.1991 Evaluate side-chains 65 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 856 ILE 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: 0.9980 chunk 57 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 44 optimal weight: 0.0270 chunk 35 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 overall best weight: 0.7638 ------------------------------------------------------------------------------- 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: 0.7448 moved from start: 0.2350 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= 0.156 Angle : 0.488 7.167 8798 Z= 0.247 Chirality : 0.038 0.144 1020 Planarity : 0.004 0.035 1019 Dihedral : 16.579 93.934 1288 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.31 % Allowed : 19.05 % Favored : 79.64 % 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: 0.65 (0.34), residues: 686 helix: 2.05 (0.38), residues: 204 sheet: 0.90 (0.42), residues: 170 loop : -0.97 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 468 HIS 0.003 0.001 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 794 ********************** 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 65 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.717 Fit side-chains REVERT: A 657 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.6398 (mtt90) REVERT: A 726 ASP cc_start: 0.7758 (p0) cc_final: 0.7487 (t0) outliers start: 8 outliers final: 7 residues processed: 62 average time/residue: 0.2021 time to fit residues: 16.7058 Evaluate side-chains 64 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 856 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 0.3980 chunk 50 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4093 r_free = 0.4093 target = 0.177412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.119822 restraints weight = 6582.555| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 3.13 r_work: 0.3289 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.2374 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= 0.158 Angle : 0.488 7.199 8798 Z= 0.247 Chirality : 0.038 0.145 1020 Planarity : 0.004 0.035 1019 Dihedral : 16.556 94.631 1288 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.48 % Allowed : 18.88 % Favored : 79.64 % 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: 0.66 (0.34), residues: 686 helix: 2.05 (0.38), residues: 204 sheet: 0.90 (0.42), residues: 170 loop : -0.96 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 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 0.005 0.000 ARG A 794 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1666.43 seconds wall clock time: 30 minutes 38.41 seconds (1838.41 seconds total)