Starting phenix.real_space_refine on Mon Mar 11 09:44:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w7t_32347/03_2024/7w7t_32347_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w7t_32347/03_2024/7w7t_32347.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w7t_32347/03_2024/7w7t_32347.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w7t_32347/03_2024/7w7t_32347.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w7t_32347/03_2024/7w7t_32347_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w7t_32347/03_2024/7w7t_32347_updated.pdb" } resolution = 3.4 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Ca 2 9.91 5 Mg 1 5.21 5 S 58 5.16 5 Be 1 3.05 5 C 5035 2.51 5 N 1318 2.21 5 O 1485 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 10": "OE1" <-> "OE2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 567": "OD1" <-> "OD2" Residue "A PHE 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 825": "OE1" <-> "OE2" Residue "A GLU 877": "OE1" <-> "OE2" Residue "A GLU 928": "OE1" <-> "OE2" Residue "A TYR 1030": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1040": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7903 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 7903 Unusual residues: {' CA': 2, ' MG': 1, 'BEF': 1} Classifications: {'peptide': 1021, 'undetermined': 4} Link IDs: {'PTRANS': 46, 'TRANS': 974, None: 4} Not linked: pdbres="SER A1042 " pdbres=" CA A4001 " Not linked: pdbres=" CA A4001 " pdbres=" CA A4002 " Not linked: pdbres=" CA A4002 " pdbres="BEF A4003 " Not linked: pdbres="BEF A4003 " pdbres=" MG A4004 " Chain breaks: 1 Time building chain proxies: 4.71, per 1000 atoms: 0.60 Number of scatterers: 7903 At special positions: 0 Unit cell: (103.335, 84.66, 138.195, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Ca 2 19.99 S 58 16.00 Mg 1 11.99 F 3 9.00 O 1485 8.00 N 1318 7.00 C 5035 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 875 " - pdb=" SG CYS A 887 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.25 Conformation dependent library (CDL) restraints added in 1.5 seconds 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1914 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 8 sheets defined 47.5% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.83 Creating SS restraints... Processing helix chain 'A' and resid 9 through 15 Processing helix chain 'A' and resid 26 through 36 Processing helix chain 'A' and resid 49 through 57 removed outlier: 4.188A pdb=" N GLN A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE A 57 " --> pdb=" O VAL A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 75 Processing helix chain 'A' and resid 90 through 121 removed outlier: 3.749A pdb=" N ILE A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU A 98 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A 118 " --> pdb=" O ASN A 114 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU A 121 " --> pdb=" O GLU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 181 No H-bonds generated for 'chain 'A' and resid 178 through 181' Processing helix chain 'A' and resid 201 through 203 No H-bonds generated for 'chain 'A' and resid 201 through 203' Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 231 through 237 removed outlier: 4.097A pdb=" N ILE A 235 " --> pdb=" O GLU A 231 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASP A 237 " --> pdb=" O GLY A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 278 removed outlier: 4.173A pdb=" N GLY A 277 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N HIS A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 305 Processing helix chain 'A' and resid 311 through 328 Processing helix chain 'A' and resid 336 through 343 removed outlier: 4.221A pdb=" N GLU A 340 " --> pdb=" O LEU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 355 No H-bonds generated for 'chain 'A' and resid 352 through 355' Processing helix chain 'A' and resid 396 through 398 No H-bonds generated for 'chain 'A' and resid 396 through 398' Processing helix chain 'A' and resid 408 through 419 Processing helix chain 'A' and resid 440 through 448 Processing helix chain 'A' and resid 467 through 470 No H-bonds generated for 'chain 'A' and resid 467 through 470' Processing helix chain 'A' and resid 473 through 477 Processing helix chain 'A' and resid 517 through 523 Processing helix chain 'A' and resid 538 through 551 Processing helix chain 'A' and resid 580 through 585 Processing helix chain 'A' and resid 604 through 616 removed outlier: 4.755A pdb=" N SER A 608 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER A 609 " --> pdb=" O GLU A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 638 Processing helix chain 'A' and resid 654 through 658 Processing helix chain 'A' and resid 662 through 671 Processing helix chain 'A' and resid 680 through 693 removed outlier: 3.847A pdb=" N PHE A 693 " --> pdb=" O PHE A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 712 removed outlier: 3.618A pdb=" N LYS A 711 " --> pdb=" O ALA A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 728 Processing helix chain 'A' and resid 739 through 780 removed outlier: 3.649A pdb=" N VAL A 743 " --> pdb=" O SER A 740 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 768 " --> pdb=" O SER A 765 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A 780 " --> pdb=" O THR A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 799 Processing helix chain 'A' and resid 801 through 808 removed outlier: 3.908A pdb=" N GLY A 807 " --> pdb=" O ALA A 803 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N PHE A 808 " --> pdb=" O THR A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 817 No H-bonds generated for 'chain 'A' and resid 815 through 817' Processing helix chain 'A' and resid 830 through 856 Processing helix chain 'A' and resid 866 through 870 Processing helix chain 'A' and resid 889 through 891 No H-bonds generated for 'chain 'A' and resid 889 through 891' Processing helix chain 'A' and resid 893 through 914 Processing helix chain 'A' and resid 926 through 928 No H-bonds generated for 'chain 'A' and resid 926 through 928' Processing helix chain 'A' and resid 930 through 947 Processing helix chain 'A' and resid 950 through 955 removed outlier: 4.493A pdb=" N LEU A 954 " --> pdb=" O GLU A 950 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE A 955 " --> pdb=" O PRO A 951 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 950 through 955' Processing helix chain 'A' and resid 963 through 989 Proline residue: A 975 - end of helix removed outlier: 3.909A pdb=" N LEU A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1029 Proline residue: A1024 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 126 through 129 Processing sheet with id= B, first strand: chain 'A' and resid 150 through 153 removed outlier: 7.210A pdb=" N ASP A 162 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 187 through 189 removed outlier: 4.819A pdb=" N LEU A 173 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ASP A 176 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ILE A 214 " --> pdb=" O ASP A 176 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 732 through 734 removed outlier: 6.125A pdb=" N VAL A 347 " --> pdb=" O ALA A 698 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N THR A 700 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N CYS A 349 " --> pdb=" O THR A 700 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ARG A 619 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N SER A 350 " --> pdb=" O ARG A 619 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE A 621 " --> pdb=" O SER A 350 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 424 through 426 Processing sheet with id= F, first strand: chain 'A' and resid 562 through 566 removed outlier: 3.750A pdb=" N SER A 495 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N THR A 499 " --> pdb=" O LYS A 481 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LYS A 481 " --> pdb=" O THR A 499 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 526 through 529 Processing sheet with id= H, first strand: chain 'A' and resid 362 through 366 removed outlier: 6.522A pdb=" N GLY A 597 " --> pdb=" O CYS A 364 " (cutoff:3.500A) 347 hydrogen bonds defined for protein. 900 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.85 Time building geometry restraints manager: 3.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2581 1.34 - 1.46: 1656 1.46 - 1.58: 3722 1.58 - 1.70: 0 1.70 - 1.82: 90 Bond restraints: 8049 Sorted by residual: bond pdb=" BE BEF A4003 " pdb=" F2 BEF A4003 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" BE BEF A4003 " pdb=" F3 BEF A4003 " ideal model delta sigma weight residual 1.476 1.547 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" BE BEF A4003 " pdb=" F1 BEF A4003 " ideal model delta sigma weight residual 1.476 1.531 -0.055 2.00e-02 2.50e+03 7.67e+00 bond pdb=" CB MET A 326 " pdb=" CG MET A 326 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.55e-01 bond pdb=" C GLU A 90 " pdb=" N PRO A 91 " ideal model delta sigma weight residual 1.335 1.347 -0.012 1.28e-02 6.10e+03 8.76e-01 ... (remaining 8044 not shown) Histogram of bond angle deviations from ideal: 98.96 - 105.97: 204 105.97 - 112.98: 4469 112.98 - 119.99: 2692 119.99 - 127.00: 3459 127.00 - 134.01: 100 Bond angle restraints: 10924 Sorted by residual: angle pdb=" N VAL A 647 " pdb=" CA VAL A 647 " pdb=" C VAL A 647 " ideal model delta sigma weight residual 111.91 107.93 3.98 8.90e-01 1.26e+00 2.00e+01 angle pdb=" F2 BEF A4003 " pdb=" BE BEF A4003 " pdb=" F3 BEF A4003 " ideal model delta sigma weight residual 119.96 107.01 12.95 3.00e+00 1.11e-01 1.86e+01 angle pdb=" F1 BEF A4003 " pdb=" BE BEF A4003 " pdb=" F3 BEF A4003 " ideal model delta sigma weight residual 120.12 109.38 10.74 3.00e+00 1.11e-01 1.28e+01 angle pdb=" N ASN A 403 " pdb=" CA ASN A 403 " pdb=" C ASN A 403 " ideal model delta sigma weight residual 114.04 109.89 4.15 1.24e+00 6.50e-01 1.12e+01 angle pdb=" C THR A 358 " pdb=" N ASN A 359 " pdb=" CA ASN A 359 " ideal model delta sigma weight residual 121.54 127.62 -6.08 1.91e+00 2.74e-01 1.01e+01 ... (remaining 10919 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.11: 4348 16.11 - 32.23: 416 32.23 - 48.34: 95 48.34 - 64.45: 14 64.45 - 80.56: 7 Dihedral angle restraints: 4880 sinusoidal: 1928 harmonic: 2952 Sorted by residual: dihedral pdb=" CG ARG A 655 " pdb=" CD ARG A 655 " pdb=" NE ARG A 655 " pdb=" CZ ARG A 655 " ideal model delta sinusoidal sigma weight residual 90.00 40.99 49.01 2 1.50e+01 4.44e-03 1.22e+01 dihedral pdb=" CA CYS A 887 " pdb=" C CYS A 887 " pdb=" N ALA A 888 " pdb=" CA ALA A 888 " ideal model delta harmonic sigma weight residual 180.00 162.70 17.30 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA ASN A 421 " pdb=" CB ASN A 421 " pdb=" CG ASN A 421 " pdb=" OD1 ASN A 421 " ideal model delta sinusoidal sigma weight residual 120.00 -165.90 -74.10 2 2.00e+01 2.50e-03 1.11e+01 ... (remaining 4877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 829 0.034 - 0.068: 307 0.068 - 0.102: 109 0.102 - 0.136: 32 0.136 - 0.170: 5 Chirality restraints: 1282 Sorted by residual: chirality pdb=" CA GLU A 90 " pdb=" N GLU A 90 " pdb=" C GLU A 90 " pdb=" CB GLU A 90 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.26e-01 chirality pdb=" CB VAL A 593 " pdb=" CA VAL A 593 " pdb=" CG1 VAL A 593 " pdb=" CG2 VAL A 593 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.97e-01 chirality pdb=" CA VAL A 129 " pdb=" N VAL A 129 " pdb=" C VAL A 129 " pdb=" CB VAL A 129 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.54e-01 ... (remaining 1279 not shown) Planarity restraints: 1392 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 855 " 0.013 2.00e-02 2.50e+03 1.26e-02 2.76e+00 pdb=" CG PHE A 855 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE A 855 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 855 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 855 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 855 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 855 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 661 " -0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO A 662 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 662 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 662 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A1016 " -0.024 5.00e-02 4.00e+02 3.58e-02 2.05e+00 pdb=" N PRO A1017 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A1017 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A1017 " -0.020 5.00e-02 4.00e+02 ... (remaining 1389 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 83 2.64 - 3.20: 7488 3.20 - 3.77: 12324 3.77 - 4.33: 16350 4.33 - 4.90: 27412 Nonbonded interactions: 63657 Sorted by model distance: nonbonded pdb=" OD2 ASP A 351 " pdb="MG MG A4004 " model vdw 2.069 2.170 nonbonded pdb=" O ASP A 351 " pdb=" OG1 THR A 355 " model vdw 2.076 2.440 nonbonded pdb=" O THR A 353 " pdb="MG MG A4004 " model vdw 2.084 2.170 nonbonded pdb=" F3 BEF A4003 " pdb="MG MG A4004 " model vdw 2.101 2.120 nonbonded pdb=" O ILE A 307 " pdb=" OE1 GLU A 309 " model vdw 2.149 3.040 ... (remaining 63652 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.210 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: 0.010 Extract box with map and model: 1.590 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 26.590 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 8049 Z= 0.198 Angle : 0.627 12.946 10924 Z= 0.336 Chirality : 0.042 0.170 1282 Planarity : 0.004 0.040 1392 Dihedral : 13.400 80.563 2963 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.11 % Allowed : 0.23 % Favored : 99.66 % 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: 0.71 (0.26), residues: 1017 helix: 1.84 (0.23), residues: 479 sheet: 0.19 (0.62), residues: 77 loop : -0.97 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 107 HIS 0.005 0.001 HIS A 526 PHE 0.029 0.001 PHE A 855 TYR 0.023 0.001 TYR A1030 ARG 0.009 0.000 ARG A 655 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 0.911 Fit side-chains REVERT: A 239 MET cc_start: 0.5346 (mpp) cc_final: 0.4393 (ttt) REVERT: A 478 LEU cc_start: 0.6884 (pp) cc_final: 0.6572 (pp) REVERT: A 566 HIS cc_start: 0.5215 (t70) cc_final: 0.4776 (t-170) REVERT: A 622 MET cc_start: 0.7726 (ttm) cc_final: 0.7488 (ttm) REVERT: A 896 MET cc_start: 0.6916 (mtm) cc_final: 0.6618 (mtm) REVERT: A 940 MET cc_start: 0.7248 (mmm) cc_final: 0.6301 (mmt) outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.2036 time to fit residues: 36.4486 Evaluate side-chains 103 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 42 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 92 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN A 251 GLN ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8049 Z= 0.164 Angle : 0.535 6.478 10924 Z= 0.280 Chirality : 0.042 0.191 1282 Planarity : 0.005 0.042 1392 Dihedral : 4.105 17.519 1081 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.26 % Allowed : 7.09 % Favored : 91.66 % 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 (0.26), residues: 1017 helix: 1.43 (0.23), residues: 492 sheet: 0.29 (0.65), residues: 68 loop : -1.07 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 272 HIS 0.002 0.001 HIS A 566 PHE 0.016 0.001 PHE A 855 TYR 0.014 0.001 TYR A 842 ARG 0.003 0.000 ARG A 572 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 103 time to evaluate : 0.971 Fit side-chains REVERT: A 109 GLU cc_start: 0.6405 (tt0) cc_final: 0.6192 (tt0) REVERT: A 239 MET cc_start: 0.5407 (mpp) cc_final: 0.4342 (ttt) REVERT: A 478 LEU cc_start: 0.6861 (pp) cc_final: 0.6585 (pp) REVERT: A 566 HIS cc_start: 0.5778 (t70) cc_final: 0.5256 (t-170) REVERT: A 940 MET cc_start: 0.7153 (mmm) cc_final: 0.6315 (mmt) outliers start: 11 outliers final: 8 residues processed: 110 average time/residue: 0.2181 time to fit residues: 32.3393 Evaluate side-chains 100 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 705 ASN Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 954 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 77 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 82 optimal weight: 0.2980 chunk 31 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1035 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8049 Z= 0.151 Angle : 0.506 6.223 10924 Z= 0.262 Chirality : 0.041 0.197 1282 Planarity : 0.004 0.042 1392 Dihedral : 4.013 19.185 1081 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.26 % Allowed : 10.29 % Favored : 88.46 % 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 (0.26), residues: 1017 helix: 1.39 (0.23), residues: 487 sheet: 0.27 (0.63), residues: 74 loop : -1.00 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 272 HIS 0.002 0.001 HIS A 566 PHE 0.012 0.001 PHE A 367 TYR 0.011 0.001 TYR A1030 ARG 0.008 0.000 ARG A 655 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 106 time to evaluate : 0.961 Fit side-chains REVERT: A 11 GLU cc_start: 0.6583 (pm20) cc_final: 0.6325 (mp0) REVERT: A 239 MET cc_start: 0.5386 (mpp) cc_final: 0.4279 (ttt) REVERT: A 453 ASN cc_start: 0.3647 (m110) cc_final: 0.3307 (t0) REVERT: A 478 LEU cc_start: 0.6927 (pp) cc_final: 0.6627 (pp) REVERT: A 566 HIS cc_start: 0.5740 (t70) cc_final: 0.5255 (t-170) REVERT: A 699 MET cc_start: 0.7318 (OUTLIER) cc_final: 0.5504 (tpt) REVERT: A 737 ASP cc_start: 0.7323 (OUTLIER) cc_final: 0.6959 (m-30) REVERT: A 940 MET cc_start: 0.7181 (mmm) cc_final: 0.6343 (mmt) REVERT: A 1030 TYR cc_start: 0.5822 (t80) cc_final: 0.5426 (t80) outliers start: 11 outliers final: 7 residues processed: 115 average time/residue: 0.2378 time to fit residues: 37.3276 Evaluate side-chains 107 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 98 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 699 MET Chi-restraints excluded: chain A residue 705 ASN Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 954 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 5.9990 chunk 48 optimal weight: 0.0980 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 88 optimal weight: 0.0670 chunk 26 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 overall best weight: 1.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 ASN ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 ASN A 767 ASN A 874 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8049 Z= 0.182 Angle : 0.518 5.498 10924 Z= 0.268 Chirality : 0.041 0.133 1282 Planarity : 0.004 0.043 1392 Dihedral : 4.077 19.712 1081 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.83 % Allowed : 11.31 % Favored : 86.86 % 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: 0.22 (0.26), residues: 1017 helix: 1.23 (0.23), residues: 495 sheet: 0.18 (0.62), residues: 74 loop : -1.09 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 272 HIS 0.003 0.001 HIS A 405 PHE 0.016 0.001 PHE A 367 TYR 0.012 0.001 TYR A 842 ARG 0.002 0.000 ARG A 614 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 0.923 Fit side-chains REVERT: A 11 GLU cc_start: 0.6543 (pm20) cc_final: 0.6294 (mp0) REVERT: A 141 LYS cc_start: 0.7015 (OUTLIER) cc_final: 0.6708 (mtpp) REVERT: A 239 MET cc_start: 0.5389 (mpp) cc_final: 0.4261 (ttt) REVERT: A 453 ASN cc_start: 0.3663 (m110) cc_final: 0.3331 (t0) REVERT: A 478 LEU cc_start: 0.7089 (pp) cc_final: 0.6825 (pp) REVERT: A 521 ILE cc_start: 0.5978 (OUTLIER) cc_final: 0.5488 (tp) REVERT: A 737 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.7073 (m-30) REVERT: A 940 MET cc_start: 0.7117 (mmm) cc_final: 0.6203 (mmt) REVERT: A 1030 TYR cc_start: 0.5781 (t80) cc_final: 0.5322 (t80) outliers start: 16 outliers final: 11 residues processed: 115 average time/residue: 0.2145 time to fit residues: 33.5447 Evaluate side-chains 110 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 96 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 705 ASN Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 954 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 19 optimal weight: 0.0570 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN A 421 ASN ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8049 Z= 0.143 Angle : 0.493 5.979 10924 Z= 0.254 Chirality : 0.041 0.210 1282 Planarity : 0.004 0.041 1392 Dihedral : 3.982 18.864 1081 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.94 % Allowed : 13.71 % Favored : 84.34 % 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: 0.20 (0.26), residues: 1017 helix: 1.19 (0.23), residues: 501 sheet: 0.12 (0.64), residues: 68 loop : -1.08 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 551 HIS 0.002 0.001 HIS A 405 PHE 0.015 0.001 PHE A 279 TYR 0.009 0.001 TYR A 842 ARG 0.002 0.000 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 99 time to evaluate : 0.850 Fit side-chains REVERT: A 239 MET cc_start: 0.5265 (mpp) cc_final: 0.4212 (ttt) REVERT: A 453 ASN cc_start: 0.3561 (m110) cc_final: 0.3319 (t0) REVERT: A 478 LEU cc_start: 0.7080 (pp) cc_final: 0.6821 (pp) REVERT: A 521 ILE cc_start: 0.6019 (OUTLIER) cc_final: 0.5524 (tp) REVERT: A 737 ASP cc_start: 0.7335 (OUTLIER) cc_final: 0.7076 (m-30) REVERT: A 940 MET cc_start: 0.7146 (mmm) cc_final: 0.6333 (mmt) REVERT: A 1030 TYR cc_start: 0.5601 (t80) cc_final: 0.5121 (t80) outliers start: 17 outliers final: 10 residues processed: 114 average time/residue: 0.1999 time to fit residues: 31.2942 Evaluate side-chains 111 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 99 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 705 ASN Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 954 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 9.9990 chunk 24 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 8 optimal weight: 0.0050 chunk 32 optimal weight: 0.0670 chunk 51 optimal weight: 10.0000 chunk 95 optimal weight: 0.0020 chunk 11 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 overall best weight: 0.3540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 ASN ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 ASN ** A 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8049 Z= 0.124 Angle : 0.477 6.544 10924 Z= 0.243 Chirality : 0.040 0.129 1282 Planarity : 0.004 0.040 1392 Dihedral : 3.831 18.966 1081 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.71 % Allowed : 15.66 % Favored : 82.63 % 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: 0.28 (0.26), residues: 1017 helix: 1.29 (0.23), residues: 500 sheet: 0.07 (0.62), residues: 68 loop : -1.08 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 793 HIS 0.003 0.001 HIS A 405 PHE 0.016 0.001 PHE A 279 TYR 0.008 0.001 TYR A 842 ARG 0.001 0.000 ARG A 572 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 105 time to evaluate : 0.894 Fit side-chains REVERT: A 235 ILE cc_start: 0.6237 (OUTLIER) cc_final: 0.6018 (mp) REVERT: A 239 MET cc_start: 0.5270 (mpp) cc_final: 0.4248 (ttt) REVERT: A 252 LYS cc_start: 0.6733 (ptmt) cc_final: 0.6434 (ptpp) REVERT: A 453 ASN cc_start: 0.3541 (m110) cc_final: 0.3341 (t0) REVERT: A 478 LEU cc_start: 0.7032 (pp) cc_final: 0.6771 (pp) REVERT: A 521 ILE cc_start: 0.6069 (OUTLIER) cc_final: 0.5504 (tp) REVERT: A 737 ASP cc_start: 0.7232 (OUTLIER) cc_final: 0.6856 (m-30) REVERT: A 877 GLU cc_start: 0.5721 (tm-30) cc_final: 0.5217 (mp0) REVERT: A 940 MET cc_start: 0.7099 (mmm) cc_final: 0.6368 (mmt) REVERT: A 990 TYR cc_start: 0.5918 (m-80) cc_final: 0.5601 (m-80) REVERT: A 1030 TYR cc_start: 0.5585 (t80) cc_final: 0.5096 (t80) outliers start: 15 outliers final: 10 residues processed: 116 average time/residue: 0.2107 time to fit residues: 33.5312 Evaluate side-chains 113 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 705 ASN Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 916 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 ASN ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8049 Z= 0.234 Angle : 0.551 6.947 10924 Z= 0.284 Chirality : 0.042 0.138 1282 Planarity : 0.004 0.038 1392 Dihedral : 4.100 18.566 1081 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.06 % Allowed : 16.80 % Favored : 81.14 % 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: 0.00 (0.26), residues: 1017 helix: 1.01 (0.23), residues: 499 sheet: 0.06 (0.60), residues: 74 loop : -1.18 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 272 HIS 0.004 0.001 HIS A 405 PHE 0.014 0.001 PHE A 367 TYR 0.013 0.001 TYR A 842 ARG 0.002 0.000 ARG A 614 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 99 time to evaluate : 0.885 Fit side-chains REVERT: A 239 MET cc_start: 0.5450 (mpp) cc_final: 0.4416 (ttt) REVERT: A 453 ASN cc_start: 0.3626 (m110) cc_final: 0.3237 (t0) REVERT: A 478 LEU cc_start: 0.7091 (pp) cc_final: 0.6835 (pp) REVERT: A 521 ILE cc_start: 0.6076 (OUTLIER) cc_final: 0.5530 (tp) REVERT: A 570 LEU cc_start: 0.3899 (OUTLIER) cc_final: 0.3638 (pp) REVERT: A 719 MET cc_start: 0.7665 (mtp) cc_final: 0.7315 (mmm) REVERT: A 737 ASP cc_start: 0.7223 (OUTLIER) cc_final: 0.6933 (m-30) REVERT: A 877 GLU cc_start: 0.5767 (tm-30) cc_final: 0.5203 (mp0) REVERT: A 940 MET cc_start: 0.7217 (mmm) cc_final: 0.6255 (mmt) REVERT: A 1030 TYR cc_start: 0.5592 (t80) cc_final: 0.5104 (t80) outliers start: 18 outliers final: 12 residues processed: 112 average time/residue: 0.2222 time to fit residues: 33.5969 Evaluate side-chains 109 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 421 ASN Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 705 ASN Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 954 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 48 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 chunk 94 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8049 Z= 0.164 Angle : 0.517 7.301 10924 Z= 0.265 Chirality : 0.041 0.131 1282 Planarity : 0.004 0.038 1392 Dihedral : 4.012 18.659 1081 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.49 % Allowed : 17.26 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.26), residues: 1017 helix: 1.14 (0.23), residues: 496 sheet: 0.15 (0.60), residues: 73 loop : -1.22 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 272 HIS 0.004 0.001 HIS A 405 PHE 0.030 0.001 PHE A 367 TYR 0.010 0.001 TYR A 842 ARG 0.002 0.000 ARG A 636 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 99 time to evaluate : 0.924 Fit side-chains REVERT: A 239 MET cc_start: 0.5453 (mpp) cc_final: 0.4431 (ttt) REVERT: A 422 ASP cc_start: 0.6280 (OUTLIER) cc_final: 0.5360 (t70) REVERT: A 453 ASN cc_start: 0.3542 (m110) cc_final: 0.3287 (t0) REVERT: A 478 LEU cc_start: 0.7064 (pp) cc_final: 0.6794 (pp) REVERT: A 719 MET cc_start: 0.7643 (mtp) cc_final: 0.7254 (mmm) REVERT: A 736 ASP cc_start: 0.6909 (p0) cc_final: 0.6707 (p0) REVERT: A 737 ASP cc_start: 0.7173 (OUTLIER) cc_final: 0.6842 (m-30) REVERT: A 806 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8306 (tt) REVERT: A 877 GLU cc_start: 0.6089 (tm-30) cc_final: 0.5501 (mp0) REVERT: A 940 MET cc_start: 0.7163 (mmm) cc_final: 0.6307 (mmt) REVERT: A 1030 TYR cc_start: 0.5586 (t80) cc_final: 0.5098 (t80) outliers start: 13 outliers final: 10 residues processed: 107 average time/residue: 0.2213 time to fit residues: 31.9803 Evaluate side-chains 110 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 705 ASN Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 916 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.0010 chunk 71 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 82 optimal weight: 0.0270 chunk 86 optimal weight: 6.9990 chunk 91 optimal weight: 0.0470 chunk 60 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 59 optimal weight: 0.2980 chunk 45 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 overall best weight: 0.2744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 ASN ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8049 Z= 0.134 Angle : 0.500 7.850 10924 Z= 0.254 Chirality : 0.040 0.126 1282 Planarity : 0.004 0.038 1392 Dihedral : 3.868 18.912 1081 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.06 % Allowed : 17.03 % Favored : 80.91 % 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: 0.23 (0.26), residues: 1017 helix: 1.29 (0.24), residues: 495 sheet: 0.11 (0.60), residues: 73 loop : -1.15 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 793 HIS 0.003 0.001 HIS A 405 PHE 0.037 0.001 PHE A 367 TYR 0.007 0.001 TYR A 842 ARG 0.002 0.000 ARG A 110 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 100 time to evaluate : 0.885 Fit side-chains REVERT: A 239 MET cc_start: 0.5461 (mpp) cc_final: 0.4435 (ttt) REVERT: A 422 ASP cc_start: 0.6212 (OUTLIER) cc_final: 0.5247 (t70) REVERT: A 453 ASN cc_start: 0.3498 (m110) cc_final: 0.3257 (t0) REVERT: A 478 LEU cc_start: 0.7036 (pp) cc_final: 0.6760 (pp) REVERT: A 521 ILE cc_start: 0.6189 (OUTLIER) cc_final: 0.5673 (tp) REVERT: A 570 LEU cc_start: 0.3873 (OUTLIER) cc_final: 0.3639 (pp) REVERT: A 719 MET cc_start: 0.7523 (mtp) cc_final: 0.7075 (mmm) REVERT: A 736 ASP cc_start: 0.6759 (p0) cc_final: 0.6508 (p0) REVERT: A 737 ASP cc_start: 0.7119 (OUTLIER) cc_final: 0.6799 (m-30) REVERT: A 877 GLU cc_start: 0.6017 (tm-30) cc_final: 0.5499 (mp0) REVERT: A 940 MET cc_start: 0.7047 (mmm) cc_final: 0.6358 (mmt) REVERT: A 1030 TYR cc_start: 0.5576 (t80) cc_final: 0.5087 (t80) outliers start: 18 outliers final: 10 residues processed: 114 average time/residue: 0.2210 time to fit residues: 34.0419 Evaluate side-chains 113 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 99 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 705 ASN Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 954 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8049 Z= 0.220 Angle : 0.566 10.429 10924 Z= 0.286 Chirality : 0.042 0.137 1282 Planarity : 0.004 0.039 1392 Dihedral : 4.067 18.194 1081 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.49 % Allowed : 17.49 % Favored : 81.03 % 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: -0.01 (0.26), residues: 1017 helix: 1.07 (0.23), residues: 498 sheet: -0.12 (0.59), residues: 74 loop : -1.23 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 272 HIS 0.005 0.001 HIS A 405 PHE 0.039 0.001 PHE A 367 TYR 0.014 0.001 TYR A 842 ARG 0.003 0.000 ARG A 636 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 0.872 Fit side-chains REVERT: A 239 MET cc_start: 0.5654 (mpp) cc_final: 0.5238 (mpp) REVERT: A 453 ASN cc_start: 0.3599 (m110) cc_final: 0.3228 (t0) REVERT: A 478 LEU cc_start: 0.7069 (pp) cc_final: 0.6818 (pp) REVERT: A 521 ILE cc_start: 0.6163 (OUTLIER) cc_final: 0.5674 (tp) REVERT: A 570 LEU cc_start: 0.3754 (OUTLIER) cc_final: 0.3440 (pp) REVERT: A 736 ASP cc_start: 0.6949 (p0) cc_final: 0.6668 (p0) REVERT: A 877 GLU cc_start: 0.6074 (tm-30) cc_final: 0.5506 (mp0) REVERT: A 940 MET cc_start: 0.7173 (mmm) cc_final: 0.6296 (mmt) REVERT: A 1030 TYR cc_start: 0.5639 (t80) cc_final: 0.5139 (t80) outliers start: 13 outliers final: 11 residues processed: 104 average time/residue: 0.2299 time to fit residues: 32.3207 Evaluate side-chains 107 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 705 ASN Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 954 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 chunk 92 optimal weight: 0.0000 chunk 54 optimal weight: 2.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.210464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.189441 restraints weight = 8736.812| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 0.85 r_work: 0.3939 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8049 Z= 0.155 Angle : 0.528 10.742 10924 Z= 0.264 Chirality : 0.040 0.128 1282 Planarity : 0.004 0.038 1392 Dihedral : 3.944 18.890 1081 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.71 % Allowed : 17.49 % Favored : 80.80 % 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: 0.10 (0.26), residues: 1017 helix: 1.22 (0.23), residues: 496 sheet: -0.00 (0.60), residues: 73 loop : -1.26 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 793 HIS 0.003 0.001 HIS A 405 PHE 0.037 0.001 PHE A 367 TYR 0.008 0.001 TYR A 842 ARG 0.001 0.000 ARG A 572 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1841.42 seconds wall clock time: 34 minutes 5.39 seconds (2045.39 seconds total)