Starting phenix.real_space_refine on Sun Mar 10 23:40:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9d_6239/03_2024/3j9d_6239.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9d_6239/03_2024/3j9d_6239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9d_6239/03_2024/3j9d_6239.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9d_6239/03_2024/3j9d_6239.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9d_6239/03_2024/3j9d_6239.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9d_6239/03_2024/3j9d_6239.pdb" } resolution = 3.3 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 ------------------------------------------------------------------------------- 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= 0.013 sd= 0.220 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 Zn 1 6.06 5 S 32 5.16 5 C 3891 2.51 5 N 1057 2.21 5 O 1105 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 2": "OD1" <-> "OD2" Residue "A GLU 3": "OE1" <-> "OE2" Residue "A GLU 22": "OE1" <-> "OE2" Residue "A GLU 54": "OE1" <-> "OE2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 141": "OD1" <-> "OD2" Residue "A ARG 175": "NH1" <-> "NH2" Residue "A GLU 177": "OE1" <-> "OE2" Residue "A GLU 437": "OE1" <-> "OE2" Residue "A GLU 480": "OE1" <-> "OE2" Residue "A ASP 498": "OD1" <-> "OD2" Residue "A PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 500": "OE1" <-> "OE2" Residue "A GLU 509": "OE1" <-> "OE2" Residue "A GLU 535": "OE1" <-> "OE2" Residue "A ASP 557": "OD1" <-> "OD2" Residue "A GLU 560": "OE1" <-> "OE2" Residue "A TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 628": "NH1" <-> "NH2" Residue "A GLU 647": "OE1" <-> "OE2" Residue "A GLU 648": "OE1" <-> "OE2" Residue "A GLU 652": "OE1" <-> "OE2" Residue "A ASP 669": "OD1" <-> "OD2" Residue "A ARG 684": "NH1" <-> "NH2" Residue "A GLU 693": "OE1" <-> "OE2" Residue "A ARG 705": "NH1" <-> "NH2" Residue "A GLU 708": "OE1" <-> "OE2" Residue "A GLU 715": "OE1" <-> "OE2" Residue "A GLU 776": "OE1" <-> "OE2" Residue "A ASP 782": "OD1" <-> "OD2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 796": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 802": "NH1" <-> "NH2" Residue "A PHE 803": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 808": "OE1" <-> "OE2" Residue "A GLU 879": "OE1" <-> "OE2" Residue "A ARG 893": "NH1" <-> "NH2" Residue "A ASP 910": "OD1" <-> "OD2" Residue "A GLU 914": "OE1" <-> "OE2" Residue "A TYR 918": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6086 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 6086 Unusual residues: {' ZN': 1} Classifications: {'peptide': 746, 'undetermined': 1} Link IDs: {'CIS': 14, 'PCIS': 2, 'PTRANS': 28, 'TRANS': 701, None: 1} Not linked: pdbres="VAL A 961 " pdbres=" ZN A1001 " Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1310 SG CYS A 162 20.064 54.313 30.963 1.00 92.09 S ATOM 3290 SG CYS A 617 23.647 56.157 31.648 1.00 70.99 S ATOM 5217 SG CYS A 851 20.362 53.869 34.614 1.00 39.61 S Time building chain proxies: 3.76, per 1000 atoms: 0.62 Number of scatterers: 6086 At special positions: 0 Unit cell: (84.84, 107.06, 81.81, 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) Zn 1 29.99 S 32 16.00 O 1105 8.00 N 1057 7.00 C 3891 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.18 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" NE2 HIS A 164 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 162 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 617 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 851 " Number of angles added : 3 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1414 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 8 sheets defined 35.9% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 40 through 43 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 74 through 85 Processing helix chain 'A' and resid 103 through 110 Processing helix chain 'A' and resid 144 through 148 removed outlier: 4.027A pdb=" N THR A 147 " --> pdb=" O LYS A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 161 Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 166 through 176 Processing helix chain 'A' and resid 412 through 416 removed outlier: 3.544A pdb=" N ASP A 415 " --> pdb=" O ASN A 412 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE A 416 " --> pdb=" O LEU A 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 412 through 416' Processing helix chain 'A' and resid 461 through 476 Processing helix chain 'A' and resid 484 through 488 removed outlier: 3.506A pdb=" N ILE A 487 " --> pdb=" O MET A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 527 Processing helix chain 'A' and resid 557 through 562 Processing helix chain 'A' and resid 589 through 596 Processing helix chain 'A' and resid 599 through 607 removed outlier: 3.917A pdb=" N ARG A 606 " --> pdb=" O GLU A 602 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG A 607 " --> pdb=" O ILE A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 638 removed outlier: 3.598A pdb=" N THR A 621 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 641 No H-bonds generated for 'chain 'A' and resid 639 through 641' Processing helix chain 'A' and resid 669 through 682 WARNING: missing atoms! Processing helix chain 'A' and resid 690 through 704 removed outlier: 3.817A pdb=" N MET A 704 " --> pdb=" O ARG A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 713 removed outlier: 3.851A pdb=" N LEU A 710 " --> pdb=" O GLY A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 725 Processing helix chain 'A' and resid 732 through 737 removed outlier: 3.998A pdb=" N ILE A 736 " --> pdb=" O VAL A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 741 Processing helix chain 'A' and resid 742 through 747 removed outlier: 4.454A pdb=" N PHE A 746 " --> pdb=" O LEU A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 791 removed outlier: 4.407A pdb=" N GLU A 791 " --> pdb=" O ILE A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 795 Processing helix chain 'A' and resid 798 through 804 Processing helix chain 'A' and resid 808 through 822 removed outlier: 4.476A pdb=" N LYS A 812 " --> pdb=" O GLU A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 837 Processing helix chain 'A' and resid 839 through 851 Processing helix chain 'A' and resid 882 through 892 Processing helix chain 'A' and resid 897 through 899 No H-bonds generated for 'chain 'A' and resid 897 through 899' Processing helix chain 'A' and resid 953 through 960 Processing sheet with id= A, first strand: chain 'A' and resid 130 through 133 removed outlier: 10.664A pdb=" N PHE A 23 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N GLY A 5 " --> pdb=" O PHE A 23 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N ILE A 25 " --> pdb=" O GLY A 5 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 4 " --> pdb=" O LEU A 942 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP A 938 " --> pdb=" O VAL A 8 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 33 through 34 removed outlier: 3.864A pdb=" N ARG A 37 " --> pdb=" O VAL A 34 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 70 through 71 Processing sheet with id= D, first strand: chain 'A' and resid 87 through 90 Processing sheet with id= E, first strand: chain 'A' and resid 149 through 150 removed outlier: 6.508A pdb=" N ILE A 871 " --> pdb=" O LEU A 901 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY A 903 " --> pdb=" O ILE A 871 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 180 through 184 Processing sheet with id= G, first strand: chain 'A' and resid 409 through 410 Processing sheet with id= H, first strand: chain 'A' and resid 760 through 765 197 hydrogen bonds defined for protein. 528 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: 1.92 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.54: 6038 1.54 - 1.90: 179 1.90 - 2.25: 3 2.25 - 2.61: 0 2.61 - 2.96: 1 Bond restraints: 6221 Sorted by residual: bond pdb=" SD MET A 771 " pdb=" CE MET A 771 " ideal model delta sigma weight residual 1.791 2.960 -1.169 2.50e-02 1.60e+03 2.19e+03 bond pdb=" CD2 TYR A 465 " pdb=" CE2 TYR A 465 " ideal model delta sigma weight residual 1.382 2.067 -0.685 3.00e-02 1.11e+03 5.21e+02 bond pdb=" CD1 TYR A 465 " pdb=" CE1 TYR A 465 " ideal model delta sigma weight residual 1.382 2.059 -0.677 3.00e-02 1.11e+03 5.10e+02 bond pdb=" CE1 TYR A 465 " pdb=" CZ TYR A 465 " ideal model delta sigma weight residual 1.378 1.812 -0.434 2.40e-02 1.74e+03 3.27e+02 bond pdb=" CE2 TYR A 465 " pdb=" CZ TYR A 465 " ideal model delta sigma weight residual 1.378 1.801 -0.423 2.40e-02 1.74e+03 3.11e+02 ... (remaining 6216 not shown) Histogram of bond angle deviations from ideal: 95.49 - 105.27: 151 105.27 - 115.06: 3692 115.06 - 124.84: 4446 124.84 - 134.63: 128 134.63 - 144.42: 3 Bond angle restraints: 8420 Sorted by residual: angle pdb=" N HIS A 16 " pdb=" CA HIS A 16 " pdb=" C HIS A 16 " ideal model delta sigma weight residual 111.11 95.49 15.62 1.20e+00 6.94e-01 1.70e+02 angle pdb=" CG MET A 771 " pdb=" SD MET A 771 " pdb=" CE MET A 771 " ideal model delta sigma weight residual 100.90 129.48 -28.58 2.20e+00 2.07e-01 1.69e+02 angle pdb=" C HIS A 653 " pdb=" N PRO A 654 " pdb=" CA PRO A 654 " ideal model delta sigma weight residual 119.84 104.48 15.36 1.25e+00 6.40e-01 1.51e+02 angle pdb=" N VAL A 27 " pdb=" CA VAL A 27 " pdb=" C VAL A 27 " ideal model delta sigma weight residual 112.29 122.07 -9.78 9.40e-01 1.13e+00 1.08e+02 angle pdb=" N GLU A 715 " pdb=" CA GLU A 715 " pdb=" C GLU A 715 " ideal model delta sigma weight residual 113.18 99.89 13.29 1.33e+00 5.65e-01 9.99e+01 ... (remaining 8415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 3047 17.68 - 35.36: 463 35.36 - 53.04: 191 53.04 - 70.72: 47 70.72 - 88.40: 8 Dihedral angle restraints: 3756 sinusoidal: 1560 harmonic: 2196 Sorted by residual: dihedral pdb=" CA VAL A 27 " pdb=" C VAL A 27 " pdb=" N GLY A 28 " pdb=" CA GLY A 28 " ideal model delta harmonic sigma weight residual 0.00 38.21 -38.21 0 5.00e+00 4.00e-02 5.84e+01 dihedral pdb=" CA HIS A 38 " pdb=" C HIS A 38 " pdb=" N ASP A 39 " pdb=" CA ASP A 39 " ideal model delta harmonic sigma weight residual -180.00 -145.72 -34.28 0 5.00e+00 4.00e-02 4.70e+01 dihedral pdb=" CA SER A 55 " pdb=" C SER A 55 " pdb=" N ILE A 56 " pdb=" CA ILE A 56 " ideal model delta harmonic sigma weight residual -180.00 -148.27 -31.73 0 5.00e+00 4.00e-02 4.03e+01 ... (remaining 3753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 749 0.101 - 0.203: 160 0.203 - 0.304: 17 0.304 - 0.405: 2 0.405 - 0.506: 1 Chirality restraints: 929 Sorted by residual: chirality pdb=" CA ASN A 63 " pdb=" N ASN A 63 " pdb=" C ASN A 63 " pdb=" CB ASN A 63 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.41e+00 chirality pdb=" CA ASN A 128 " pdb=" N ASN A 128 " pdb=" C ASN A 128 " pdb=" CB ASN A 128 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CB ILE A 670 " pdb=" CA ILE A 670 " pdb=" CG1 ILE A 670 " pdb=" CG2 ILE A 670 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.36e+00 ... (remaining 926 not shown) Planarity restraints: 1078 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 618 " -0.018 2.00e-02 2.50e+03 3.60e-02 1.29e+01 pdb=" C PRO A 618 " 0.062 2.00e-02 2.50e+03 pdb=" O PRO A 618 " -0.023 2.00e-02 2.50e+03 pdb=" N THR A 619 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 653 " 0.057 5.00e-02 4.00e+02 8.58e-02 1.18e+01 pdb=" N PRO A 654 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO A 654 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 654 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 16 " 0.016 2.00e-02 2.50e+03 3.34e-02 1.11e+01 pdb=" C HIS A 16 " -0.058 2.00e-02 2.50e+03 pdb=" O HIS A 16 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU A 17 " 0.019 2.00e-02 2.50e+03 ... (remaining 1075 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 158 2.61 - 3.18: 5710 3.18 - 3.75: 9704 3.75 - 4.33: 13753 4.33 - 4.90: 21601 Nonbonded interactions: 50926 Sorted by model distance: nonbonded pdb=" O ASN A 47 " pdb=" ND2 ASN A 47 " model vdw 2.034 2.520 nonbonded pdb=" O PHE A 803 " pdb=" N LYS A 805 " model vdw 2.131 2.520 nonbonded pdb=" NE ARG A 74 " pdb=" OD2 ASP A 114 " model vdw 2.162 2.520 nonbonded pdb=" N GLU A 184 " pdb=" OE1 GLU A 184 " model vdw 2.234 2.520 nonbonded pdb=" OG1 THR A 506 " pdb=" N THR A 507 " model vdw 2.247 2.520 ... (remaining 50921 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: 0.170 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: 1.040 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 21.970 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 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 : 0.027 1.169 6221 Z= 1.945 Angle : 2.044 28.578 8420 Z= 1.291 Chirality : 0.083 0.506 929 Planarity : 0.009 0.086 1078 Dihedral : 20.567 88.397 2342 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 23.66 Ramachandran Plot: Outliers : 2.16 % Allowed : 8.22 % Favored : 89.62 % Rotamer: Outliers : 24.92 % Allowed : 16.97 % Favored : 58.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 1.82 % Twisted Proline : 0.00 % Twisted General : 0.84 % 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: -3.64 (0.29), residues: 742 helix: -3.11 (0.25), residues: 222 sheet: -2.97 (0.37), residues: 153 loop : -1.54 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.004 TRP A 107 HIS 0.015 0.003 HIS A 653 PHE 0.036 0.005 PHE A 23 TYR 0.038 0.005 TYR A 827 ARG 0.007 0.001 ARG A 709 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 144 time to evaluate : 0.678 Fit side-chains TARDY: cannot create tardy model for: "SER A 671 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 15 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8628 (tt0) REVERT: A 22 GLU cc_start: 0.9444 (tt0) cc_final: 0.9192 (tt0) REVERT: A 56 ILE cc_start: 0.9492 (OUTLIER) cc_final: 0.9055 (tp) REVERT: A 118 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9292 (mt) REVERT: A 119 LYS cc_start: 0.9358 (OUTLIER) cc_final: 0.8890 (tttp) REVERT: A 156 GLU cc_start: 0.7009 (pt0) cc_final: 0.4953 (tt0) REVERT: A 168 MET cc_start: 0.9255 (OUTLIER) cc_final: 0.9017 (tpp) REVERT: A 413 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9118 (mt) REVERT: A 467 GLN cc_start: 0.8661 (mt0) cc_final: 0.8316 (tt0) REVERT: A 486 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8949 (mtmt) REVERT: A 501 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.6839 (mmtp) REVERT: A 529 LYS cc_start: 0.8998 (tttm) cc_final: 0.8794 (ttpt) REVERT: A 540 ARG cc_start: 0.8091 (ptp90) cc_final: 0.7401 (ptm-80) REVERT: A 552 SER cc_start: 0.9261 (t) cc_final: 0.8927 (p) REVERT: A 576 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.8985 (mt) REVERT: A 577 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.8520 (ttm170) REVERT: A 584 GLN cc_start: 0.9327 (OUTLIER) cc_final: 0.8569 (tt0) REVERT: A 606 ARG cc_start: 0.9541 (OUTLIER) cc_final: 0.9340 (mtp-110) REVERT: A 625 THR cc_start: 0.9687 (OUTLIER) cc_final: 0.9347 (m) REVERT: A 627 GLU cc_start: 0.9489 (OUTLIER) cc_final: 0.8786 (tm-30) REVERT: A 638 GLN cc_start: 0.9522 (OUTLIER) cc_final: 0.9246 (mt0) REVERT: A 641 VAL cc_start: 0.9394 (t) cc_final: 0.9065 (m) REVERT: A 681 ILE cc_start: 0.9537 (OUTLIER) cc_final: 0.9256 (mp) REVERT: A 687 ARG cc_start: 0.9119 (ttm110) cc_final: 0.8892 (ttm-80) REVERT: A 692 TYR cc_start: 0.9546 (m-80) cc_final: 0.9315 (m-80) REVERT: A 704 MET cc_start: 0.9360 (OUTLIER) cc_final: 0.9106 (mmm) REVERT: A 733 VAL cc_start: 0.9325 (OUTLIER) cc_final: 0.8975 (t) REVERT: A 758 GLN cc_start: 0.8957 (mt0) cc_final: 0.8575 (mt0) REVERT: A 769 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7055 (pm20) REVERT: A 784 CYS cc_start: 0.8758 (OUTLIER) cc_final: 0.7992 (p) REVERT: A 818 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8847 (tp) REVERT: A 819 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.8966 (tttp) REVERT: A 842 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9251 (tp) REVERT: A 879 GLU cc_start: 0.8813 (tp30) cc_final: 0.8510 (tm-30) REVERT: A 934 LYS cc_start: 0.9317 (OUTLIER) cc_final: 0.8385 (ttmt) REVERT: A 959 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9286 (mt) outliers start: 166 outliers final: 72 residues processed: 273 average time/residue: 0.2390 time to fit residues: 80.4606 Evaluate side-chains 210 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 113 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 16 HIS Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 486 LYS Chi-restraints excluded: chain A residue 501 LYS Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 584 GLN Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 606 ARG Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 638 GLN Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 679 ASP Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain A residue 708 GLU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 757 ARG Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 769 GLU Chi-restraints excluded: chain A residue 784 CYS Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 819 LYS Chi-restraints excluded: chain A residue 823 ASN Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 839 LYS Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 856 ASP Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 929 LYS Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 961 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 HIS ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 672 GLN A 947 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 1.163 6221 Z= 1.638 Angle : 0.878 28.971 8420 Z= 0.446 Chirality : 0.047 0.173 929 Planarity : 0.005 0.049 1078 Dihedral : 14.905 59.295 1033 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.67 % Allowed : 7.14 % Favored : 92.18 % Rotamer: Outliers : 12.46 % Allowed : 20.57 % Favored : 66.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 1.96 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.54 (0.28), residues: 742 helix: -1.35 (0.31), residues: 222 sheet: -1.99 (0.41), residues: 134 loop : -1.72 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 61 HIS 0.008 0.002 HIS A 658 PHE 0.021 0.002 PHE A 796 TYR 0.026 0.002 TYR A 62 ARG 0.003 0.001 ARG A 802 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 147 time to evaluate : 0.767 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "SER A 671 " (corrupted residue). Skipping it. REVERT: A 156 GLU cc_start: 0.6220 (pt0) cc_final: 0.4777 (tt0) REVERT: A 168 MET cc_start: 0.9174 (tmm) cc_final: 0.8892 (tpp) REVERT: A 487 ILE cc_start: 0.9361 (pt) cc_final: 0.9149 (pt) REVERT: A 501 LYS cc_start: 0.7163 (OUTLIER) cc_final: 0.6849 (mmtp) REVERT: A 540 ARG cc_start: 0.8055 (ptp90) cc_final: 0.7502 (ptm-80) REVERT: A 560 GLU cc_start: 0.8488 (tp30) cc_final: 0.8183 (tt0) REVERT: A 592 GLU cc_start: 0.8221 (tm-30) cc_final: 0.8017 (tm-30) REVERT: A 692 TYR cc_start: 0.9250 (m-80) cc_final: 0.8649 (m-80) REVERT: A 798 SER cc_start: 0.8774 (m) cc_final: 0.8397 (p) REVERT: A 810 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8148 (mt0) REVERT: A 819 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8641 (tttm) REVERT: A 959 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9157 (mt) outliers start: 83 outliers final: 44 residues processed: 214 average time/residue: 0.1846 time to fit residues: 51.2000 Evaluate side-chains 161 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 113 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 16 HIS Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 501 LYS Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 658 HIS Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 810 GLN Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 819 LYS Chi-restraints excluded: chain A residue 823 ASN Chi-restraints excluded: chain A residue 856 ASP Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 961 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 55 optimal weight: 8.9990 chunk 45 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 59 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 chunk 22 optimal weight: 0.1980 chunk 54 optimal weight: 0.3980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 ASN A 485 HIS ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 672 GLN A 735 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 1.165 6221 Z= 1.641 Angle : 0.808 28.698 8420 Z= 0.412 Chirality : 0.047 0.179 929 Planarity : 0.004 0.035 1078 Dihedral : 11.701 59.789 906 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.67 % Allowed : 7.95 % Favored : 91.37 % Rotamer: Outliers : 8.86 % Allowed : 23.57 % Favored : 67.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 1.96 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.20 (0.29), residues: 742 helix: -0.65 (0.33), residues: 220 sheet: -1.96 (0.39), residues: 134 loop : -1.73 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 61 HIS 0.004 0.001 HIS A 658 PHE 0.017 0.002 PHE A 796 TYR 0.020 0.002 TYR A 62 ARG 0.005 0.000 ARG A 597 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 121 time to evaluate : 0.701 Fit side-chains TARDY: cannot create tardy model for: "SER A 671 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 15 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8404 (tt0) REVERT: A 156 GLU cc_start: 0.6330 (pt0) cc_final: 0.4940 (tt0) REVERT: A 168 MET cc_start: 0.9152 (tmm) cc_final: 0.8866 (tpp) REVERT: A 177 GLU cc_start: 0.9013 (OUTLIER) cc_final: 0.8801 (mt-10) REVERT: A 487 ILE cc_start: 0.9356 (pt) cc_final: 0.9151 (pt) REVERT: A 501 LYS cc_start: 0.7103 (OUTLIER) cc_final: 0.6829 (mmtp) REVERT: A 540 ARG cc_start: 0.8195 (ptp90) cc_final: 0.7613 (ptm-80) REVERT: A 692 TYR cc_start: 0.9277 (m-80) cc_final: 0.8659 (m-80) REVERT: A 793 MET cc_start: 0.9056 (mmm) cc_final: 0.8731 (mmm) REVERT: A 798 SER cc_start: 0.8792 (m) cc_final: 0.8456 (p) REVERT: A 810 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8553 (mt0) REVERT: A 819 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8571 (tttm) REVERT: A 844 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8706 (mt-10) outliers start: 59 outliers final: 43 residues processed: 169 average time/residue: 0.1802 time to fit residues: 39.9730 Evaluate side-chains 159 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 111 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 501 LYS Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 663 PHE Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 810 GLN Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 819 LYS Chi-restraints excluded: chain A residue 823 ASN Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 856 ASP Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 956 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 32 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 35 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 ASN ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 672 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 1.165 6221 Z= 1.632 Angle : 0.753 28.400 8420 Z= 0.381 Chirality : 0.045 0.184 929 Planarity : 0.004 0.030 1078 Dihedral : 10.668 59.534 894 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.67 % Allowed : 7.14 % Favored : 92.18 % Rotamer: Outliers : 9.31 % Allowed : 23.57 % Favored : 67.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 1.96 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.03 (0.29), residues: 742 helix: -0.19 (0.34), residues: 222 sheet: -2.25 (0.39), residues: 134 loop : -1.67 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.008 0.001 HIS A 658 PHE 0.016 0.001 PHE A 796 TYR 0.019 0.001 TYR A 62 ARG 0.002 0.000 ARG A 886 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 129 time to evaluate : 0.730 Fit side-chains TARDY: cannot create tardy model for: "SER A 671 " (corrupted residue). Skipping it. REVERT: A 15 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8298 (tt0) REVERT: A 16 HIS cc_start: 0.5234 (OUTLIER) cc_final: 0.4611 (t70) REVERT: A 38 HIS cc_start: 0.8459 (OUTLIER) cc_final: 0.8142 (p90) REVERT: A 106 GLN cc_start: 0.8898 (mm-40) cc_final: 0.8521 (mt0) REVERT: A 110 LYS cc_start: 0.9006 (ptmt) cc_final: 0.8730 (ttpp) REVERT: A 156 GLU cc_start: 0.6618 (pt0) cc_final: 0.5091 (mt-10) REVERT: A 168 MET cc_start: 0.9116 (tmm) cc_final: 0.8849 (tpp) REVERT: A 467 GLN cc_start: 0.8550 (mt0) cc_final: 0.8334 (tt0) REVERT: A 487 ILE cc_start: 0.9339 (pt) cc_final: 0.9125 (pt) REVERT: A 501 LYS cc_start: 0.7335 (OUTLIER) cc_final: 0.6865 (mmtp) REVERT: A 540 ARG cc_start: 0.8166 (ptp90) cc_final: 0.7632 (ptm-80) REVERT: A 692 TYR cc_start: 0.9216 (m-80) cc_final: 0.8623 (m-80) REVERT: A 789 TYR cc_start: 0.9199 (t80) cc_final: 0.8966 (t80) REVERT: A 793 MET cc_start: 0.8993 (mmm) cc_final: 0.8712 (mmm) REVERT: A 798 SER cc_start: 0.8714 (m) cc_final: 0.8348 (p) REVERT: A 810 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8186 (mt0) REVERT: A 819 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8525 (tttm) REVERT: A 844 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8676 (mt-10) REVERT: A 929 LYS cc_start: 0.9236 (mmmt) cc_final: 0.8870 (mmtt) outliers start: 62 outliers final: 41 residues processed: 178 average time/residue: 0.1881 time to fit residues: 43.4931 Evaluate side-chains 162 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 115 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 16 HIS Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 501 LYS Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 810 GLN Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 819 LYS Chi-restraints excluded: chain A residue 823 ASN Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 856 ASP Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 877 SER Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 956 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 29 optimal weight: 20.0000 chunk 61 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 18 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 672 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 1.166 6221 Z= 1.664 Angle : 0.820 28.405 8420 Z= 0.416 Chirality : 0.049 0.176 929 Planarity : 0.004 0.040 1078 Dihedral : 10.615 59.638 885 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.54 % Allowed : 8.89 % Favored : 90.57 % Rotamer: Outliers : 8.86 % Allowed : 22.82 % Favored : 68.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 1.96 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.19 (0.29), residues: 742 helix: -0.38 (0.33), residues: 227 sheet: -2.16 (0.37), residues: 144 loop : -1.80 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 107 HIS 0.005 0.001 HIS A 653 PHE 0.017 0.002 PHE A 796 TYR 0.020 0.002 TYR A 62 ARG 0.008 0.001 ARG A 597 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 112 time to evaluate : 0.780 Fit side-chains TARDY: cannot create tardy model for: "SER A 671 " (corrupted residue). Skipping it. REVERT: A 16 HIS cc_start: 0.5486 (OUTLIER) cc_final: 0.4940 (t70) REVERT: A 18 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8668 (mp) REVERT: A 38 HIS cc_start: 0.8685 (OUTLIER) cc_final: 0.8289 (p90) REVERT: A 106 GLN cc_start: 0.8885 (mm-40) cc_final: 0.8616 (mt0) REVERT: A 156 GLU cc_start: 0.7210 (pt0) cc_final: 0.5472 (mp0) REVERT: A 168 MET cc_start: 0.9175 (tmm) cc_final: 0.8915 (tpp) REVERT: A 467 GLN cc_start: 0.8542 (mt0) cc_final: 0.8305 (tt0) REVERT: A 487 ILE cc_start: 0.9363 (pt) cc_final: 0.9140 (pt) REVERT: A 501 LYS cc_start: 0.7442 (OUTLIER) cc_final: 0.6965 (mmtp) REVERT: A 540 ARG cc_start: 0.8278 (ptp90) cc_final: 0.7582 (ptm-80) REVERT: A 599 ASP cc_start: 0.8108 (t0) cc_final: 0.7788 (t0) REVERT: A 692 TYR cc_start: 0.9363 (m-80) cc_final: 0.8793 (m-80) REVERT: A 784 CYS cc_start: 0.8341 (OUTLIER) cc_final: 0.8081 (p) REVERT: A 793 MET cc_start: 0.9007 (mmm) cc_final: 0.8756 (mmm) REVERT: A 798 SER cc_start: 0.8836 (m) cc_final: 0.8512 (p) REVERT: A 810 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8318 (mt0) REVERT: A 844 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8675 (mt-10) outliers start: 59 outliers final: 42 residues processed: 161 average time/residue: 0.1869 time to fit residues: 39.2251 Evaluate side-chains 150 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 102 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 16 HIS Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 501 LYS Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 784 CYS Chi-restraints excluded: chain A residue 810 GLN Chi-restraints excluded: chain A residue 823 ASN Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 856 ASP Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 877 SER Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 956 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 71 optimal weight: 0.0980 chunk 59 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 23 optimal weight: 0.2980 chunk 37 optimal weight: 7.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 ASN ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 672 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 1.164 6221 Z= 1.630 Angle : 0.725 28.519 8420 Z= 0.369 Chirality : 0.044 0.177 929 Planarity : 0.004 0.034 1078 Dihedral : 9.811 59.482 878 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.54 % Allowed : 6.33 % Favored : 93.13 % Rotamer: Outliers : 6.91 % Allowed : 25.83 % Favored : 67.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 1.96 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.29), residues: 742 helix: 0.02 (0.34), residues: 228 sheet: -1.75 (0.43), residues: 114 loop : -1.78 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 104 HIS 0.003 0.001 HIS A 534 PHE 0.016 0.001 PHE A 796 TYR 0.021 0.001 TYR A 62 ARG 0.004 0.000 ARG A 597 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 124 time to evaluate : 0.646 Fit side-chains TARDY: cannot create tardy model for: "SER A 671 " (corrupted residue). Skipping it. REVERT: A 16 HIS cc_start: 0.5351 (OUTLIER) cc_final: 0.4157 (t-90) REVERT: A 38 HIS cc_start: 0.8399 (OUTLIER) cc_final: 0.8120 (p90) REVERT: A 106 GLN cc_start: 0.8890 (mm-40) cc_final: 0.8608 (mt0) REVERT: A 156 GLU cc_start: 0.7241 (pt0) cc_final: 0.5735 (mt-10) REVERT: A 168 MET cc_start: 0.9089 (tmm) cc_final: 0.8832 (tpp) REVERT: A 467 GLN cc_start: 0.8519 (mt0) cc_final: 0.8272 (tt0) REVERT: A 487 ILE cc_start: 0.9334 (pt) cc_final: 0.9103 (pt) REVERT: A 501 LYS cc_start: 0.7315 (OUTLIER) cc_final: 0.6862 (mmtp) REVERT: A 540 ARG cc_start: 0.8244 (ptp90) cc_final: 0.7593 (ptm-80) REVERT: A 599 ASP cc_start: 0.7893 (t0) cc_final: 0.6647 (t0) REVERT: A 692 TYR cc_start: 0.9240 (m-80) cc_final: 0.8610 (m-80) REVERT: A 789 TYR cc_start: 0.9152 (t80) cc_final: 0.8852 (t80) REVERT: A 798 SER cc_start: 0.8710 (m) cc_final: 0.8384 (p) REVERT: A 810 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8248 (mt0) REVERT: A 844 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8666 (mt-10) outliers start: 46 outliers final: 37 residues processed: 157 average time/residue: 0.1914 time to fit residues: 39.0196 Evaluate side-chains 151 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 110 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 16 HIS Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 501 LYS Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 757 ARG Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 810 GLN Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 823 ASN Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 856 ASP Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 956 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 0.8980 chunk 8 optimal weight: 7.9990 chunk 40 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 433 HIS ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 1.163 6221 Z= 1.637 Angle : 0.741 28.526 8420 Z= 0.375 Chirality : 0.045 0.195 929 Planarity : 0.004 0.039 1078 Dihedral : 9.696 59.742 876 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.67 % Allowed : 7.68 % Favored : 91.64 % Rotamer: Outliers : 7.51 % Allowed : 25.83 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 1.96 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.30), residues: 742 helix: 0.09 (0.35), residues: 228 sheet: -1.65 (0.44), residues: 114 loop : -1.73 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 107 HIS 0.005 0.001 HIS A 640 PHE 0.015 0.001 PHE A 796 TYR 0.018 0.001 TYR A 62 ARG 0.006 0.000 ARG A 628 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 116 time to evaluate : 0.714 Fit side-chains TARDY: cannot create tardy model for: "SER A 671 " (corrupted residue). Skipping it. REVERT: A 16 HIS cc_start: 0.5360 (OUTLIER) cc_final: 0.4139 (t-90) REVERT: A 38 HIS cc_start: 0.8434 (OUTLIER) cc_final: 0.8160 (p90) REVERT: A 156 GLU cc_start: 0.7353 (pt0) cc_final: 0.7123 (pt0) REVERT: A 168 MET cc_start: 0.9091 (tmm) cc_final: 0.8824 (tpp) REVERT: A 467 GLN cc_start: 0.8534 (mt0) cc_final: 0.8280 (tt0) REVERT: A 487 ILE cc_start: 0.9336 (pt) cc_final: 0.9099 (pt) REVERT: A 692 TYR cc_start: 0.9294 (m-80) cc_final: 0.8655 (m-80) REVERT: A 789 TYR cc_start: 0.9153 (t80) cc_final: 0.8809 (t80) REVERT: A 798 SER cc_start: 0.8788 (m) cc_final: 0.8443 (p) REVERT: A 810 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8279 (mt0) REVERT: A 844 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8605 (mt-10) REVERT: A 934 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8765 (ttmt) outliers start: 50 outliers final: 39 residues processed: 153 average time/residue: 0.1807 time to fit residues: 36.9596 Evaluate side-chains 153 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 110 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 16 HIS Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 757 ARG Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 810 GLN Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 823 ASN Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 856 ASP Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 956 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 1.164 6221 Z= 1.659 Angle : 0.807 28.428 8420 Z= 0.407 Chirality : 0.048 0.194 929 Planarity : 0.004 0.044 1078 Dihedral : 9.738 58.902 869 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.67 % Allowed : 8.89 % Favored : 90.43 % Rotamer: Outliers : 7.06 % Allowed : 25.98 % Favored : 66.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 1.96 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.30), residues: 742 helix: -0.19 (0.33), residues: 230 sheet: -1.61 (0.42), residues: 124 loop : -1.80 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 107 HIS 0.004 0.001 HIS A 38 PHE 0.017 0.002 PHE A 796 TYR 0.017 0.002 TYR A 62 ARG 0.004 0.000 ARG A 597 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 105 time to evaluate : 0.703 Fit side-chains TARDY: cannot create tardy model for: "SER A 671 " (corrupted residue). Skipping it. REVERT: A 16 HIS cc_start: 0.5525 (OUTLIER) cc_final: 0.4989 (t70) REVERT: A 18 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8718 (mp) REVERT: A 38 HIS cc_start: 0.8537 (OUTLIER) cc_final: 0.8200 (p90) REVERT: A 168 MET cc_start: 0.9121 (tmm) cc_final: 0.8820 (tpp) REVERT: A 467 GLN cc_start: 0.8487 (mt0) cc_final: 0.8261 (tt0) REVERT: A 487 ILE cc_start: 0.9348 (pt) cc_final: 0.9115 (pt) REVERT: A 692 TYR cc_start: 0.9388 (m-80) cc_final: 0.8859 (m-80) REVERT: A 789 TYR cc_start: 0.9238 (t80) cc_final: 0.8930 (t80) REVERT: A 798 SER cc_start: 0.8857 (m) cc_final: 0.8530 (p) REVERT: A 810 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.8336 (mt0) REVERT: A 844 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8680 (mt-10) REVERT: A 934 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8740 (ttmt) outliers start: 47 outliers final: 38 residues processed: 143 average time/residue: 0.1787 time to fit residues: 33.6780 Evaluate side-chains 142 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 99 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 16 HIS Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 757 ARG Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 810 GLN Chi-restraints excluded: chain A residue 823 ASN Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 856 ASP Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 877 SER Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 956 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 68 optimal weight: 0.2980 chunk 40 optimal weight: 6.9990 chunk 28 optimal weight: 0.2980 chunk 52 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 1.163 6221 Z= 1.631 Angle : 0.728 28.574 8420 Z= 0.369 Chirality : 0.044 0.182 929 Planarity : 0.004 0.047 1078 Dihedral : 9.224 59.003 869 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.93 % Favored : 93.53 % Rotamer: Outliers : 6.76 % Allowed : 25.98 % Favored : 67.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 1.96 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.30), residues: 742 helix: 0.12 (0.35), residues: 228 sheet: -1.51 (0.45), residues: 114 loop : -1.72 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 104 HIS 0.003 0.001 HIS A 534 PHE 0.015 0.001 PHE A 796 TYR 0.017 0.001 TYR A 49 ARG 0.002 0.000 ARG A 783 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 113 time to evaluate : 0.755 Fit side-chains TARDY: cannot create tardy model for: "SER A 671 " (corrupted residue). Skipping it. REVERT: A 16 HIS cc_start: 0.5312 (OUTLIER) cc_final: 0.4101 (t-90) REVERT: A 38 HIS cc_start: 0.8350 (OUTLIER) cc_final: 0.8126 (p90) REVERT: A 110 LYS cc_start: 0.8956 (ptmt) cc_final: 0.8695 (ttpp) REVERT: A 168 MET cc_start: 0.9083 (tmm) cc_final: 0.8813 (tpp) REVERT: A 467 GLN cc_start: 0.8498 (mt0) cc_final: 0.8268 (tt0) REVERT: A 487 ILE cc_start: 0.9318 (pt) cc_final: 0.9088 (pt) REVERT: A 501 LYS cc_start: 0.7424 (OUTLIER) cc_final: 0.7036 (mmtp) REVERT: A 686 ARG cc_start: 0.9124 (mtt-85) cc_final: 0.8710 (mtp85) REVERT: A 692 TYR cc_start: 0.9307 (m-80) cc_final: 0.8761 (m-80) REVERT: A 798 SER cc_start: 0.8797 (m) cc_final: 0.8436 (p) REVERT: A 810 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8303 (mt0) REVERT: A 875 GLU cc_start: 0.9102 (OUTLIER) cc_final: 0.8177 (tm-30) REVERT: A 934 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8771 (ttmt) outliers start: 45 outliers final: 35 residues processed: 147 average time/residue: 0.1802 time to fit residues: 34.7603 Evaluate side-chains 147 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 106 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 16 HIS Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 501 LYS Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 757 ARG Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 810 GLN Chi-restraints excluded: chain A residue 813 ILE Chi-restraints excluded: chain A residue 823 ASN Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 856 ASP Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 877 SER Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 934 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 0.0570 chunk 46 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 1.162 6221 Z= 1.631 Angle : 0.724 28.666 8420 Z= 0.365 Chirality : 0.044 0.172 929 Planarity : 0.004 0.047 1078 Dihedral : 8.745 59.414 868 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.54 % Allowed : 7.28 % Favored : 92.18 % Rotamer: Outliers : 5.71 % Allowed : 26.73 % Favored : 67.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 1.96 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.31), residues: 742 helix: 0.22 (0.36), residues: 229 sheet: -1.21 (0.47), residues: 112 loop : -1.67 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.005 0.001 HIS A 433 PHE 0.015 0.001 PHE A 796 TYR 0.018 0.001 TYR A 49 ARG 0.005 0.000 ARG A 628 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 116 time to evaluate : 0.793 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "SER A 671 " (corrupted residue). Skipping it. REVERT: A 16 HIS cc_start: 0.5218 (OUTLIER) cc_final: 0.4137 (t-90) REVERT: A 110 LYS cc_start: 0.8970 (ptmt) cc_final: 0.8712 (ttpp) REVERT: A 168 MET cc_start: 0.9019 (tmm) cc_final: 0.8669 (tpp) REVERT: A 467 GLN cc_start: 0.8515 (mt0) cc_final: 0.8298 (tt0) REVERT: A 487 ILE cc_start: 0.9282 (pt) cc_final: 0.9024 (pt) REVERT: A 501 LYS cc_start: 0.7363 (OUTLIER) cc_final: 0.7021 (mmtp) REVERT: A 686 ARG cc_start: 0.9096 (mtt-85) cc_final: 0.8722 (mtp85) REVERT: A 692 TYR cc_start: 0.9264 (m-80) cc_final: 0.8671 (m-80) REVERT: A 789 TYR cc_start: 0.8974 (t80) cc_final: 0.8665 (t80) REVERT: A 798 SER cc_start: 0.8786 (m) cc_final: 0.8419 (p) REVERT: A 810 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8518 (mt0) REVERT: A 934 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8766 (ttmt) outliers start: 38 outliers final: 30 residues processed: 145 average time/residue: 0.1906 time to fit residues: 36.0182 Evaluate side-chains 144 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 110 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 16 HIS Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 501 LYS Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 757 ARG Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 810 GLN Chi-restraints excluded: chain A residue 823 ASN Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 856 ASP Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 877 SER Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 934 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 1.9990 chunk 8 optimal weight: 0.0270 chunk 16 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.9242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.111488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.095079 restraints weight = 8664.453| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.68 r_work: 0.2896 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 1.164 6221 Z= 1.634 Angle : 0.732 28.481 8420 Z= 0.368 Chirality : 0.044 0.170 929 Planarity : 0.004 0.049 1078 Dihedral : 8.359 59.672 863 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.54 % Allowed : 6.74 % Favored : 92.72 % Rotamer: Outliers : 5.41 % Allowed : 27.78 % Favored : 66.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 1.96 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.31), residues: 742 helix: 0.29 (0.36), residues: 229 sheet: -0.90 (0.49), residues: 108 loop : -1.68 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 107 HIS 0.003 0.001 HIS A 433 PHE 0.016 0.001 PHE A 663 TYR 0.018 0.001 TYR A 49 ARG 0.005 0.000 ARG A 597 =============================================================================== Job complete usr+sys time: 1734.16 seconds wall clock time: 31 minutes 58.28 seconds (1918.28 seconds total)