Starting phenix.real_space_refine on Thu Dec 7 23:36:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2a_27830/12_2023/8e2a_27830.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2a_27830/12_2023/8e2a_27830.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2a_27830/12_2023/8e2a_27830.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2a_27830/12_2023/8e2a_27830.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2a_27830/12_2023/8e2a_27830.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e2a_27830/12_2023/8e2a_27830.pdb" } resolution = 2.8 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= 0.021 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 15 5.49 5 S 31 5.16 5 C 3621 2.51 5 N 985 2.21 5 O 1116 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 ASP 91": "OD1" <-> "OD2" Residue "A ASP 109": "OD1" <-> "OD2" Residue "A TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 240": "OE1" <-> "OE2" Residue "A ARG 263": "NH1" <-> "NH2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 292": "NH1" <-> "NH2" Residue "A PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 307": "OD1" <-> "OD2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "A GLU 328": "OE1" <-> "OE2" Residue "A GLU 334": "OE1" <-> "OE2" Residue "A ASP 343": "OD1" <-> "OD2" Residue "A ASP 346": "OD1" <-> "OD2" Residue "A ASP 373": "OD1" <-> "OD2" Residue "A PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 389": "OD1" <-> "OD2" Residue "A ASP 401": "OD1" <-> "OD2" Residue "A PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 512": "OE1" <-> "OE2" Residue "A ASP 561": "OD1" <-> "OD2" Residue "A GLU 563": "OE1" <-> "OE2" Residue "A TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 659": "OE1" <-> "OE2" Residue "A TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 721": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 741": "OD1" <-> "OD2" Residue "A GLU 751": "OE1" <-> "OE2" Residue "A PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 769": "OE1" <-> "OE2" Residue "A PHE 807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 823": "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: 5768 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 686, 5456 Classifications: {'peptide': 686} Link IDs: {'PTRANS': 40, 'TRANS': 645} Chain breaks: 2 Chain: "B" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 312 Classifications: {'RNA': 15} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 13} Chain breaks: 1 Time building chain proxies: 3.47, per 1000 atoms: 0.60 Number of scatterers: 5768 At special positions: 0 Unit cell: (70.35, 84.42, 109.21, 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 15 15.00 O 1116 8.00 N 985 7.00 C 3621 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: 1.90 Conformation dependent library (CDL) restraints added in 1.0 seconds 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1310 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 9 sheets defined 32.9% alpha, 22.9% beta 4 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 55 through 66 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 292 through 297 removed outlier: 3.730A pdb=" N ALA A 297 " --> pdb=" O LYS A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 340 removed outlier: 3.664A pdb=" N GLU A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Proline residue: A 331 - end of helix removed outlier: 3.712A pdb=" N TYR A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 431 Processing helix chain 'A' and resid 445 through 451 Processing helix chain 'A' and resid 494 through 502 removed outlier: 3.587A pdb=" N GLN A 498 " --> pdb=" O TYR A 494 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER A 499 " --> pdb=" O GLU A 495 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET A 500 " --> pdb=" O HIS A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 513 Processing helix chain 'A' and resid 522 through 546 removed outlier: 3.666A pdb=" N ALA A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE A 535 " --> pdb=" O ASN A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 601 removed outlier: 3.671A pdb=" N PHE A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 629 removed outlier: 3.775A pdb=" N LEU A 618 " --> pdb=" O GLN A 614 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER A 619 " --> pdb=" O THR A 615 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASP A 620 " --> pdb=" O ARG A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 646 Processing helix chain 'A' and resid 651 through 666 removed outlier: 3.800A pdb=" N LEU A 655 " --> pdb=" O ASP A 651 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ALA A 656 " --> pdb=" O LYS A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 687 removed outlier: 3.519A pdb=" N PHE A 686 " --> pdb=" O PRO A 683 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG A 687 " --> pdb=" O ALA A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 719 removed outlier: 3.817A pdb=" N VAL A 709 " --> pdb=" O ARG A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 766 removed outlier: 3.646A pdb=" N THR A 754 " --> pdb=" O GLN A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 800 No H-bonds generated for 'chain 'A' and resid 798 through 800' Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 72 removed outlier: 7.335A pdb=" N LEU A 110 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ILE A 238 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL A 112 " --> pdb=" O VAL A 236 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 75 Processing sheet with id=AA3, first strand: chain 'A' and resid 556 through 560 removed outlier: 3.954A pdb=" N GLY A 569 " --> pdb=" O THR A 559 " (cutoff:3.500A) removed outlier: 9.118A pdb=" N GLN A 568 " --> pdb=" O ILE A 302 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ILE A 302 " --> pdb=" O GLN A 568 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU A 316 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU A 319 " --> pdb=" O PRO A 281 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 372 through 373 removed outlier: 4.012A pdb=" N ASP A 478 " --> pdb=" O THR A 469 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 380 through 383 removed outlier: 6.157A pdb=" N THR A 381 " --> pdb=" O LEU A 492 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 434 through 435 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 791 through 796 removed outlier: 3.636A pdb=" N VAL A 791 " --> pdb=" O VAL A 786 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ALA A 781 " --> pdb=" O ILE A 777 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ILE A 777 " --> pdb=" O ALA A 781 " (cutoff:3.500A) removed outlier: 6.683A 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 810 238 hydrogen bonds defined for protein. 663 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 12 hydrogen bonds 24 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 1.88 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1662 1.33 - 1.45: 928 1.45 - 1.57: 3253 1.57 - 1.69: 28 1.69 - 1.81: 47 Bond restraints: 5918 Sorted by residual: bond pdb=" C ARG A 616 " pdb=" O ARG A 616 " ideal model delta sigma weight residual 1.235 1.217 0.019 1.26e-02 6.30e+03 2.16e+00 bond pdb=" C LEU A 359 " pdb=" N PRO A 360 " ideal model delta sigma weight residual 1.334 1.362 -0.028 2.34e-02 1.83e+03 1.40e+00 bond pdb=" CA GLY A 811 " pdb=" C GLY A 811 " ideal model delta sigma weight residual 1.514 1.530 -0.015 1.41e-02 5.03e+03 1.21e+00 bond pdb=" CG LEU A 423 " pdb=" CD1 LEU A 423 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.19e+00 bond pdb=" C ARG A 616 " pdb=" N MET A 617 " ideal model delta sigma weight residual 1.335 1.321 0.014 1.35e-02 5.49e+03 1.10e+00 ... (remaining 5913 not shown) Histogram of bond angle deviations from ideal: 99.02 - 106.01: 234 106.01 - 113.00: 3179 113.00 - 119.99: 2038 119.99 - 126.98: 2533 126.98 - 133.97: 90 Bond angle restraints: 8074 Sorted by residual: angle pdb=" C LYS A 812 " pdb=" N LYS A 813 " pdb=" CA LYS A 813 " ideal model delta sigma weight residual 121.61 126.86 -5.25 1.39e+00 5.18e-01 1.43e+01 angle pdb=" N MET A 617 " pdb=" CA MET A 617 " pdb=" C MET A 617 " ideal model delta sigma weight residual 112.38 116.17 -3.79 1.22e+00 6.72e-01 9.65e+00 angle pdb=" C ARG A 616 " pdb=" CA ARG A 616 " pdb=" CB ARG A 616 " ideal model delta sigma weight residual 110.42 115.90 -5.48 1.99e+00 2.53e-01 7.59e+00 angle pdb=" C THR A 615 " pdb=" N ARG A 616 " pdb=" CA ARG A 616 " ideal model delta sigma weight residual 121.54 126.34 -4.80 1.91e+00 2.74e-01 6.31e+00 angle pdb=" N SER A 848 " pdb=" CA SER A 848 " pdb=" C SER A 848 " ideal model delta sigma weight residual 111.02 114.01 -2.99 1.22e+00 6.72e-01 5.99e+00 ... (remaining 8069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 3327 17.71 - 35.42: 241 35.42 - 53.13: 36 53.13 - 70.83: 20 70.83 - 88.54: 11 Dihedral angle restraints: 3635 sinusoidal: 1623 harmonic: 2012 Sorted by residual: dihedral pdb=" CA ASP A 824 " pdb=" C ASP A 824 " pdb=" N MET A 825 " pdb=" CA MET A 825 " ideal model delta harmonic sigma weight residual -180.00 -158.71 -21.29 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA LEU A 673 " pdb=" C LEU A 673 " pdb=" N TYR A 674 " pdb=" CA TYR A 674 " ideal model delta harmonic sigma weight residual 180.00 160.41 19.59 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA PHE A 699 " pdb=" C PHE A 699 " pdb=" N THR A 700 " pdb=" CA THR A 700 " ideal model delta harmonic sigma weight residual -180.00 -160.84 -19.16 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 3632 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 764 0.062 - 0.124: 145 0.124 - 0.186: 13 0.186 - 0.248: 0 0.248 - 0.310: 1 Chirality restraints: 923 Sorted by residual: chirality pdb=" CG LEU A 618 " pdb=" CB LEU A 618 " pdb=" CD1 LEU A 618 " pdb=" CD2 LEU A 618 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CA ARG A 616 " pdb=" N ARG A 616 " pdb=" C ARG A 616 " pdb=" CB ARG A 616 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.57e-01 chirality pdb=" CA HIS A 409 " pdb=" N HIS A 409 " pdb=" C HIS A 409 " pdb=" CB HIS A 409 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.12e-01 ... (remaining 920 not shown) Planarity restraints: 990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 610 " 0.031 5.00e-02 4.00e+02 4.76e-02 3.62e+00 pdb=" N PRO A 611 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 611 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 611 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 634 " 0.013 2.00e-02 2.50e+03 1.09e-02 2.09e+00 pdb=" CG PHE A 634 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 634 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 634 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 634 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 634 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 634 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 648 " 0.007 2.00e-02 2.50e+03 1.07e-02 2.00e+00 pdb=" CG PHE A 648 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE A 648 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 648 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 648 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 648 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 648 " -0.000 2.00e-02 2.50e+03 ... (remaining 987 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 226 2.72 - 3.26: 5283 3.26 - 3.81: 8564 3.81 - 4.35: 11167 4.35 - 4.90: 19247 Nonbonded interactions: 44487 Sorted by model distance: nonbonded pdb=" OH TYR A 575 " pdb=" OE1 GLU A 583 " model vdw 2.173 2.440 nonbonded pdb=" OD1 ASP A 651 " pdb=" N LYS A 652 " model vdw 2.182 2.520 nonbonded pdb=" ND1 HIS A 409 " pdb=" OG SER A 465 " model vdw 2.249 2.520 nonbonded pdb=" OD2 ASP A 307 " pdb=" NZ LYS A 309 " model vdw 2.283 2.520 nonbonded pdb=" OD2 ASP A 412 " pdb=" NH1 ARG A 483 " model vdw 2.314 2.520 ... (remaining 44482 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: 1.310 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: 6.110 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 19.380 Find NCS groups from input model: 0.150 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:14.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 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 : 0.004 0.038 5918 Z= 0.279 Angle : 0.709 8.103 8074 Z= 0.379 Chirality : 0.047 0.310 923 Planarity : 0.005 0.048 990 Dihedral : 13.879 88.543 2325 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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: -0.21 (0.31), residues: 680 helix: 1.18 (0.36), residues: 208 sheet: 0.34 (0.38), residues: 161 loop : -1.32 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 468 HIS 0.005 0.001 HIS A 409 PHE 0.025 0.002 PHE A 634 TYR 0.018 0.002 TYR A 853 ARG 0.007 0.001 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.591 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 1.5383 time to fit residues: 148.3771 Evaluate side-chains 52 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.688 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5918 Z= 0.182 Angle : 0.570 9.618 8074 Z= 0.284 Chirality : 0.042 0.144 923 Planarity : 0.004 0.039 990 Dihedral : 10.573 73.019 957 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.49 % Allowed : 8.96 % Favored : 89.55 % 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: 0.14 (0.32), residues: 680 helix: 1.67 (0.37), residues: 209 sheet: 0.21 (0.38), residues: 170 loop : -1.11 (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 243 PHE 0.014 0.002 PHE A 648 TYR 0.009 0.001 TYR A 674 ARG 0.005 0.000 ARG A 803 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 59 time to evaluate : 0.648 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 64 average time/residue: 1.1985 time to fit residues: 80.7124 Evaluate side-chains 60 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 0.671 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.0542 time to fit residues: 1.0170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 8.9990 chunk 19 optimal weight: 0.0980 chunk 52 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 21 optimal weight: 0.0770 chunk 50 optimal weight: 0.8980 chunk 47 optimal weight: 0.4980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 ASN A 553 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5918 Z= 0.128 Angle : 0.502 8.625 8074 Z= 0.251 Chirality : 0.040 0.145 923 Planarity : 0.004 0.031 990 Dihedral : 10.356 73.152 957 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.33 % Allowed : 9.95 % Favored : 88.72 % 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 (0.32), residues: 680 helix: 2.19 (0.37), residues: 205 sheet: 0.32 (0.38), residues: 168 loop : -0.93 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 468 HIS 0.002 0.000 HIS A 243 PHE 0.017 0.001 PHE A 80 TYR 0.008 0.001 TYR A 674 ARG 0.004 0.000 ARG A 803 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.609 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 60 average time/residue: 1.2115 time to fit residues: 76.5475 Evaluate side-chains 54 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 0.674 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.0541 time to fit residues: 1.1202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 32 optimal weight: 4.9990 chunk 6 optimal weight: 0.0970 chunk 29 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 17 optimal weight: 0.0070 chunk 55 optimal weight: 0.7980 chunk 37 optimal weight: 0.4980 chunk 0 optimal weight: 6.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- 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: 0.7551 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5918 Z= 0.124 Angle : 0.487 7.537 8074 Z= 0.243 Chirality : 0.040 0.142 923 Planarity : 0.004 0.030 990 Dihedral : 10.241 73.157 957 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.33 % Allowed : 11.28 % Favored : 87.40 % 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: 0.67 (0.32), residues: 680 helix: 2.39 (0.37), residues: 205 sheet: 0.34 (0.38), residues: 168 loop : -0.86 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 468 HIS 0.001 0.000 HIS A 688 PHE 0.016 0.001 PHE A 80 TYR 0.007 0.001 TYR A 674 ARG 0.003 0.000 ARG A 803 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 53 time to evaluate : 0.692 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 57 average time/residue: 1.2832 time to fit residues: 76.8399 Evaluate side-chains 54 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 51 time to evaluate : 0.673 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.0546 time to fit residues: 0.9782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5918 Z= 0.225 Angle : 0.559 8.000 8074 Z= 0.275 Chirality : 0.043 0.145 923 Planarity : 0.004 0.037 990 Dihedral : 10.240 73.132 957 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.66 % Allowed : 11.44 % Favored : 86.90 % 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 (0.32), residues: 680 helix: 2.06 (0.37), residues: 209 sheet: 0.28 (0.38), residues: 170 loop : -0.96 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 468 HIS 0.003 0.001 HIS A 712 PHE 0.015 0.002 PHE A 80 TYR 0.008 0.001 TYR A 575 ARG 0.003 0.000 ARG A 550 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 51 time to evaluate : 0.587 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 57 average time/residue: 1.4110 time to fit residues: 84.0888 Evaluate side-chains 58 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 51 time to evaluate : 0.651 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 3 average time/residue: 0.1136 time to fit residues: 1.4305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 66 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 0.0870 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.8764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 663 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5918 Z= 0.167 Angle : 0.516 7.394 8074 Z= 0.258 Chirality : 0.041 0.142 923 Planarity : 0.004 0.033 990 Dihedral : 10.160 73.159 957 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.82 % Allowed : 12.11 % Favored : 86.07 % 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: 0.59 (0.33), residues: 680 helix: 2.14 (0.37), residues: 211 sheet: 0.42 (0.39), residues: 162 loop : -0.87 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 468 HIS 0.002 0.001 HIS A 571 PHE 0.017 0.001 PHE A 80 TYR 0.007 0.001 TYR A 674 ARG 0.004 0.000 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 51 time to evaluate : 0.667 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 57 average time/residue: 1.4183 time to fit residues: 84.6481 Evaluate side-chains 58 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 50 time to evaluate : 0.618 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 3 average time/residue: 0.1095 time to fit residues: 1.3030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 48 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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: 0.7607 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5918 Z= 0.163 Angle : 0.522 10.068 8074 Z= 0.257 Chirality : 0.041 0.136 923 Planarity : 0.004 0.033 990 Dihedral : 10.113 73.150 957 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.66 % Allowed : 12.44 % Favored : 85.90 % 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: 0.51 (0.33), residues: 680 helix: 1.99 (0.37), residues: 217 sheet: 0.31 (0.38), residues: 170 loop : -0.90 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 468 HIS 0.002 0.001 HIS A 571 PHE 0.016 0.001 PHE A 80 TYR 0.007 0.001 TYR A 674 ARG 0.004 0.000 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 53 time to evaluate : 0.686 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 59 average time/residue: 1.3759 time to fit residues: 85.0038 Evaluate side-chains 56 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 50 time to evaluate : 0.566 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 2 average time/residue: 0.1547 time to fit residues: 1.3037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 12 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 6 optimal weight: 0.2980 chunk 52 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 chunk 61 optimal weight: 0.0270 chunk 37 optimal weight: 2.9990 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 ASN A 614 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5918 Z= 0.143 Angle : 0.518 10.308 8074 Z= 0.259 Chirality : 0.041 0.159 923 Planarity : 0.004 0.032 990 Dihedral : 10.090 73.165 957 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.66 % Allowed : 12.77 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.33), residues: 680 helix: 2.07 (0.37), residues: 217 sheet: 0.31 (0.38), residues: 170 loop : -0.82 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 468 HIS 0.002 0.000 HIS A 571 PHE 0.016 0.001 PHE A 80 TYR 0.007 0.001 TYR A 674 ARG 0.003 0.000 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 51 time to evaluate : 0.655 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 56 average time/residue: 1.2399 time to fit residues: 73.0995 Evaluate side-chains 56 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 48 time to evaluate : 0.629 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 4 average time/residue: 0.1307 time to fit residues: 1.6913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 26 optimal weight: 0.7980 chunk 48 optimal weight: 7.9990 chunk 19 optimal weight: 0.0870 chunk 56 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 40 optimal weight: 5.9990 chunk 65 optimal weight: 50.0000 chunk 39 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 45 optimal weight: 0.0170 overall best weight: 0.4996 ------------------------------------------------------------------------------- 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: 0.7568 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5918 Z= 0.133 Angle : 0.505 11.338 8074 Z= 0.251 Chirality : 0.040 0.133 923 Planarity : 0.004 0.033 990 Dihedral : 10.054 73.174 957 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.00 % Allowed : 13.76 % Favored : 85.24 % 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: 0.69 (0.33), residues: 680 helix: 2.17 (0.37), residues: 217 sheet: 0.30 (0.39), residues: 170 loop : -0.75 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 468 HIS 0.001 0.000 HIS A 571 PHE 0.016 0.001 PHE A 80 TYR 0.007 0.001 TYR A 674 ARG 0.005 0.000 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 0.602 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 56 average time/residue: 1.3685 time to fit residues: 80.2310 Evaluate side-chains 54 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 0.637 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 1.0812 time to fit residues: 2.0066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 20.0000 chunk 63 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 ASN A 681 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5918 Z= 0.201 Angle : 0.565 11.572 8074 Z= 0.281 Chirality : 0.042 0.163 923 Planarity : 0.004 0.034 990 Dihedral : 10.098 73.148 957 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.16 % Allowed : 13.93 % Favored : 84.91 % 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 (0.33), residues: 680 helix: 1.98 (0.37), residues: 217 sheet: 0.26 (0.39), residues: 170 loop : -0.83 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 468 HIS 0.003 0.001 HIS A 712 PHE 0.018 0.002 PHE A 80 TYR 0.007 0.001 TYR A 674 ARG 0.004 0.000 ARG A 74 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 50 time to evaluate : 0.691 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 53 average time/residue: 1.4073 time to fit residues: 77.9244 Evaluate side-chains 50 residues out of total 603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.537 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.0536 time to fit residues: 0.9399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 15 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 22 optimal weight: 0.1980 chunk 56 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.155983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.113248 restraints weight = 6273.211| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.37 r_work: 0.3241 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5918 Z= 0.153 Angle : 0.533 11.622 8074 Z= 0.267 Chirality : 0.041 0.167 923 Planarity : 0.004 0.032 990 Dihedral : 10.085 73.165 957 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.66 % Allowed : 14.26 % Favored : 85.07 % 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: 0.64 (0.33), residues: 680 helix: 2.08 (0.37), residues: 217 sheet: 0.31 (0.39), residues: 170 loop : -0.77 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 468 HIS 0.004 0.001 HIS A 562 PHE 0.018 0.001 PHE A 80 TYR 0.007 0.001 TYR A 53 ARG 0.004 0.000 ARG A 803 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2391.01 seconds wall clock time: 43 minutes 14.78 seconds (2594.78 seconds total)