Starting phenix.real_space_refine on Mon Mar 11 02:44:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yam_33717/03_2024/7yam_33717_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yam_33717/03_2024/7yam_33717.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/7yam_33717/03_2024/7yam_33717.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yam_33717/03_2024/7yam_33717.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yam_33717/03_2024/7yam_33717_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yam_33717/03_2024/7yam_33717_updated.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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.109 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: 7 Type Number sf(0) Gaussians Mg 1 5.21 5 S 52 5.16 5 Be 1 3.05 5 C 4254 2.51 5 N 1116 2.21 5 O 1245 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 50": "OE1" <-> "OE2" Residue "A PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 451": "OE1" <-> "OE2" Residue "A TYR 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 532": "OE1" <-> "OE2" Residue "A PHE 815": "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: 6672 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 873, 6672 Unusual residues: {' MG': 1, 'BEF': 1} Classifications: {'peptide': 871, 'undetermined': 2} Link IDs: {'PTRANS': 34, 'TRANS': 836, None: 2} Not linked: pdbres="LYS A 904 " pdbres="BEF A1001 " Not linked: pdbres="BEF A1001 " pdbres=" MG A1002 " Chain breaks: 3 Time building chain proxies: 4.16, per 1000 atoms: 0.62 Number of scatterers: 6672 At special positions: 0 Unit cell: (80.5359, 86.3718, 130.725, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 52 16.00 Mg 1 11.99 F 3 9.00 O 1245 8.00 N 1116 7.00 C 4254 6.00 Be 1 4.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.75 Conformation dependent library (CDL) restraints added in 1.1 seconds 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1622 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 33 helices and 7 sheets defined 51.1% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 23 through 28 Processing helix chain 'A' and resid 31 through 38 Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 72 through 80 removed outlier: 3.800A pdb=" N GLN A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N PHE A 79 " --> pdb=" O TYR A 75 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LYS A 80 " --> pdb=" O ILE A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 96 Processing helix chain 'A' and resid 100 through 121 Processing helix chain 'A' and resid 186 through 189 No H-bonds generated for 'chain 'A' and resid 186 through 189' Processing helix chain 'A' and resid 240 through 250 Processing helix chain 'A' and resid 257 through 287 Processing helix chain 'A' and resid 291 through 305 removed outlier: 3.991A pdb=" N SER A 300 " --> pdb=" O THR A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 327 removed outlier: 4.329A pdb=" N ILE A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 342 removed outlier: 4.130A pdb=" N LEU A 341 " --> pdb=" O VAL A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 410 Processing helix chain 'A' and resid 425 through 437 Processing helix chain 'A' and resid 440 through 442 No H-bonds generated for 'chain 'A' and resid 440 through 442' Processing helix chain 'A' and resid 483 through 489 Processing helix chain 'A' and resid 504 through 520 Processing helix chain 'A' and resid 552 through 561 Processing helix chain 'A' and resid 574 through 584 Processing helix chain 'A' and resid 596 through 601 Processing helix chain 'A' and resid 604 through 611 Processing helix chain 'A' and resid 622 through 634 Processing helix chain 'A' and resid 646 through 654 removed outlier: 4.684A pdb=" N VAL A 650 " --> pdb=" O ASN A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 672 Processing helix chain 'A' and resid 683 through 722 Processing helix chain 'A' and resid 731 through 751 removed outlier: 3.740A pdb=" N MET A 741 " --> pdb=" O ILE A 737 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP A 742 " --> pdb=" O ASN A 738 " (cutoff:3.500A) Proline residue: A 744 - end of helix removed outlier: 4.315A pdb=" N VAL A 751 " --> pdb=" O GLN A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 759 No H-bonds generated for 'chain 'A' and resid 756 through 759' Processing helix chain 'A' and resid 773 through 797 Processing helix chain 'A' and resid 805 through 825 Processing helix chain 'A' and resid 833 through 836 No H-bonds generated for 'chain 'A' and resid 833 through 836' Processing helix chain 'A' and resid 842 through 860 Processing helix chain 'A' and resid 862 through 868 Processing helix chain 'A' and resid 875 through 903 removed outlier: 4.134A pdb=" N SER A 887 " --> pdb=" O GLY A 883 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N VAL A 888 " --> pdb=" O LEU A 884 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N CYS A 889 " --> pdb=" O THR A 885 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 160 through 163 removed outlier: 4.085A pdb=" N LYS A 227 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 179 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL A 231 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N LEU A 175 " --> pdb=" O VAL A 231 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 181 through 183 removed outlier: 4.850A pdb=" N LEU A 181 " --> pdb=" O LYS A 197 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 330 through 332 removed outlier: 3.615A pdb=" N MET A 661 " --> pdb=" O GLY A 643 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL A 346 " --> pdb=" O ALA A 640 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N THR A 642 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N CYS A 348 " --> pdb=" O THR A 642 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N SER A 565 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N SER A 349 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LYS A 567 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 391 through 393 removed outlier: 4.376A pdb=" N VAL A 386 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N THR A 363 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLY A 543 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ILE A 365 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU A 541 " --> pdb=" O ILE A 365 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N THR A 367 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N LEU A 539 " --> pdb=" O THR A 367 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU A 527 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU A 541 " --> pdb=" O LEU A 525 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU A 525 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLY A 543 " --> pdb=" O ARG A 523 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ARG A 523 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA A 462 " --> pdb=" O TYR A 452 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA A 450 " --> pdb=" O LYS A 464 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL A 466 " --> pdb=" O ARG A 448 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ARG A 448 " --> pdb=" O VAL A 466 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 415 through 417 Processing sheet with id= F, first strand: chain 'A' and resid 498 through 501 removed outlier: 7.333A pdb=" N LEU A 536 " --> pdb=" O THR A 491 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N TYR A 493 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N PHE A 538 " --> pdb=" O TYR A 493 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N SER A 495 " --> pdb=" O PHE A 538 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 593 through 595 removed outlier: 6.668A pdb=" N VAL A 616 " --> pdb=" O VAL A 594 " (cutoff:3.500A) No H-bonds generated for sheet with id= G 354 hydrogen bonds defined for protein. 1008 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.20 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2147 1.34 - 1.46: 779 1.46 - 1.58: 3765 1.58 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 6775 Sorted by residual: bond pdb=" BE BEF A1001 " pdb=" F2 BEF A1001 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" BE BEF A1001 " pdb=" F3 BEF A1001 " ideal model delta sigma weight residual 1.476 1.544 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" N GLN A 747 " pdb=" CA GLN A 747 " ideal model delta sigma weight residual 1.456 1.497 -0.040 1.31e-02 5.83e+03 9.51e+00 bond pdb=" BE BEF A1001 " pdb=" F1 BEF A1001 " ideal model delta sigma weight residual 1.476 1.538 -0.062 2.00e-02 2.50e+03 9.47e+00 bond pdb=" CB PRO A 531 " pdb=" CG PRO A 531 " ideal model delta sigma weight residual 1.492 1.571 -0.079 5.00e-02 4.00e+02 2.52e+00 ... (remaining 6770 not shown) Histogram of bond angle deviations from ideal: 99.43 - 106.35: 180 106.35 - 113.28: 3858 113.28 - 120.20: 2290 120.20 - 127.12: 2785 127.12 - 134.05: 55 Bond angle restraints: 9168 Sorted by residual: angle pdb=" F2 BEF A1001 " pdb=" BE BEF A1001 " pdb=" F3 BEF A1001 " ideal model delta sigma weight residual 119.96 106.19 13.77 3.00e+00 1.11e-01 2.11e+01 angle pdb=" F1 BEF A1001 " pdb=" BE BEF A1001 " pdb=" F3 BEF A1001 " ideal model delta sigma weight residual 120.12 109.70 10.42 3.00e+00 1.11e-01 1.21e+01 angle pdb=" C ASN A 738 " pdb=" N ILE A 739 " pdb=" CA ILE A 739 " ideal model delta sigma weight residual 122.97 119.83 3.14 9.80e-01 1.04e+00 1.03e+01 angle pdb=" C ASN A 701 " pdb=" N PHE A 702 " pdb=" CA PHE A 702 " ideal model delta sigma weight residual 121.14 116.52 4.62 1.75e+00 3.27e-01 6.96e+00 angle pdb=" N GLN A 747 " pdb=" CA GLN A 747 " pdb=" CB GLN A 747 " ideal model delta sigma weight residual 110.41 114.70 -4.29 1.68e+00 3.54e-01 6.53e+00 ... (remaining 9163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 3661 16.82 - 33.65: 374 33.65 - 50.47: 77 50.47 - 67.29: 11 67.29 - 84.11: 11 Dihedral angle restraints: 4134 sinusoidal: 1629 harmonic: 2505 Sorted by residual: dihedral pdb=" CA CYS A 225 " pdb=" C CYS A 225 " pdb=" N GLY A 226 " pdb=" CA GLY A 226 " ideal model delta harmonic sigma weight residual -180.00 -155.27 -24.73 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA GLY A 226 " pdb=" C GLY A 226 " pdb=" N LYS A 227 " pdb=" CA LYS A 227 " ideal model delta harmonic sigma weight residual 180.00 -163.23 -16.77 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CB MET A 661 " pdb=" CG MET A 661 " pdb=" SD MET A 661 " pdb=" CE MET A 661 " ideal model delta sinusoidal sigma weight residual 180.00 121.25 58.75 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 4131 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 735 0.033 - 0.066: 264 0.066 - 0.099: 69 0.099 - 0.132: 33 0.132 - 0.165: 2 Chirality restraints: 1103 Sorted by residual: chirality pdb=" CA PHE A 702 " pdb=" N PHE A 702 " pdb=" C PHE A 702 " pdb=" CB PHE A 702 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" CA ILE A 657 " pdb=" N ILE A 657 " pdb=" C ILE A 657 " pdb=" CB ILE A 657 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CA PRO A 531 " pdb=" N PRO A 531 " pdb=" C PRO A 531 " pdb=" CB PRO A 531 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 1100 not shown) Planarity restraints: 1155 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 747 " 0.016 2.00e-02 2.50e+03 3.37e-02 1.14e+01 pdb=" C GLN A 747 " -0.058 2.00e-02 2.50e+03 pdb=" O GLN A 747 " 0.022 2.00e-02 2.50e+03 pdb=" N SER A 748 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 136 " -0.026 5.00e-02 4.00e+02 3.91e-02 2.44e+00 pdb=" N PRO A 137 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 137 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 137 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 743 " -0.026 5.00e-02 4.00e+02 3.85e-02 2.38e+00 pdb=" N PRO A 744 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 744 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 744 " -0.021 5.00e-02 4.00e+02 ... (remaining 1152 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 10 2.39 - 3.01: 3747 3.01 - 3.64: 10189 3.64 - 4.27: 14900 4.27 - 4.90: 25806 Nonbonded interactions: 54652 Sorted by model distance: nonbonded pdb=" F1 BEF A1001 " pdb="MG MG A1002 " model vdw 1.756 2.120 nonbonded pdb=" OD2 ASP A 350 " pdb="MG MG A1002 " model vdw 1.997 2.170 nonbonded pdb=" O ASP A 350 " pdb=" OG1 THR A 354 " model vdw 2.106 2.440 nonbonded pdb=" O THR A 352 " pdb="MG MG A1002 " model vdw 2.132 2.170 nonbonded pdb=" OD1 ASP A 644 " pdb="MG MG A1002 " model vdw 2.200 2.170 ... (remaining 54647 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: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.720 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 22.130 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 6775 Z= 0.231 Angle : 0.535 13.773 9168 Z= 0.272 Chirality : 0.040 0.165 1103 Planarity : 0.004 0.039 1155 Dihedral : 14.474 84.113 2512 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.13 % Allowed : 0.40 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.29), residues: 863 helix: 2.36 (0.24), residues: 478 sheet: -0.15 (0.55), residues: 87 loop : 0.05 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 460 HIS 0.005 0.001 HIS A 149 PHE 0.024 0.002 PHE A 702 TYR 0.006 0.001 TYR A 380 ARG 0.002 0.000 ARG A 623 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 0.739 Fit side-chains REVERT: A 25 LYS cc_start: 0.7991 (mmmt) cc_final: 0.7007 (mttm) REVERT: A 28 GLU cc_start: 0.6929 (mt-10) cc_final: 0.6677 (mp0) REVERT: A 54 ARG cc_start: 0.7331 (mtt90) cc_final: 0.7106 (mtt90) REVERT: A 464 LYS cc_start: 0.8154 (mtmm) cc_final: 0.7536 (mtmm) outliers start: 1 outliers final: 1 residues processed: 128 average time/residue: 0.1891 time to fit residues: 32.2436 Evaluate side-chains 104 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 747 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 0.0770 chunk 65 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.0817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6775 Z= 0.234 Angle : 0.485 6.489 9168 Z= 0.254 Chirality : 0.040 0.165 1103 Planarity : 0.004 0.039 1155 Dihedral : 4.736 71.473 919 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.20 % Allowed : 8.16 % Favored : 90.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.29), residues: 863 helix: 2.28 (0.24), residues: 477 sheet: -0.25 (0.54), residues: 86 loop : 0.06 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 736 HIS 0.002 0.001 HIS A 149 PHE 0.023 0.002 PHE A 702 TYR 0.022 0.001 TYR A 75 ARG 0.001 0.000 ARG A 704 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 103 time to evaluate : 0.769 Fit side-chains REVERT: A 25 LYS cc_start: 0.7982 (mmmt) cc_final: 0.7709 (mttm) REVERT: A 464 LYS cc_start: 0.8330 (mtmm) cc_final: 0.8037 (mttp) REVERT: A 735 LEU cc_start: 0.8533 (mt) cc_final: 0.8199 (mt) outliers start: 9 outliers final: 8 residues processed: 107 average time/residue: 0.1839 time to fit residues: 26.6154 Evaluate side-chains 106 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 895 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 6775 Z= 0.267 Angle : 0.500 6.623 9168 Z= 0.260 Chirality : 0.040 0.168 1103 Planarity : 0.004 0.043 1155 Dihedral : 3.948 20.930 916 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.27 % Allowed : 9.89 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.29), residues: 863 helix: 2.14 (0.24), residues: 476 sheet: -0.06 (0.60), residues: 71 loop : 0.07 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 736 HIS 0.001 0.001 HIS A 364 PHE 0.022 0.002 PHE A 702 TYR 0.018 0.001 TYR A 75 ARG 0.002 0.000 ARG A 760 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 99 time to evaluate : 0.784 Fit side-chains REVERT: A 25 LYS cc_start: 0.8019 (mmmt) cc_final: 0.7228 (mttm) REVERT: A 449 LYS cc_start: 0.8659 (mmtp) cc_final: 0.8092 (mmtm) REVERT: A 464 LYS cc_start: 0.8384 (mtmm) cc_final: 0.8059 (mttp) REVERT: A 606 GLN cc_start: 0.7463 (tp40) cc_final: 0.7187 (tp40) REVERT: A 735 LEU cc_start: 0.8560 (mt) cc_final: 0.8237 (mt) REVERT: A 853 MET cc_start: 0.7701 (mmm) cc_final: 0.7429 (mmm) outliers start: 17 outliers final: 11 residues processed: 106 average time/residue: 0.1903 time to fit residues: 27.1160 Evaluate side-chains 106 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 895 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 41 optimal weight: 0.0040 chunk 8 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 79 optimal weight: 0.0070 chunk 84 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 70 optimal weight: 0.3980 overall best weight: 0.3410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 GLN A 485 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 6775 Z= 0.156 Angle : 0.456 6.758 9168 Z= 0.237 Chirality : 0.038 0.153 1103 Planarity : 0.004 0.043 1155 Dihedral : 3.743 20.159 916 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.87 % Allowed : 11.90 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.29), residues: 863 helix: 2.34 (0.24), residues: 475 sheet: -0.52 (0.51), residues: 92 loop : 0.16 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 460 HIS 0.002 0.000 HIS A 149 PHE 0.024 0.001 PHE A 702 TYR 0.016 0.001 TYR A 75 ARG 0.001 0.000 ARG A 704 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 105 time to evaluate : 0.802 Fit side-chains REVERT: A 25 LYS cc_start: 0.8172 (mmmt) cc_final: 0.7694 (mttm) REVERT: A 449 LYS cc_start: 0.8663 (mmtp) cc_final: 0.8256 (mmtm) REVERT: A 464 LYS cc_start: 0.8397 (mtmm) cc_final: 0.8062 (mttm) REVERT: A 735 LEU cc_start: 0.8458 (mt) cc_final: 0.8111 (mt) REVERT: A 828 SER cc_start: 0.8386 (t) cc_final: 0.8159 (m) REVERT: A 853 MET cc_start: 0.7632 (mmm) cc_final: 0.7390 (mmm) outliers start: 14 outliers final: 10 residues processed: 110 average time/residue: 0.1932 time to fit residues: 28.4843 Evaluate side-chains 108 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 895 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 42 optimal weight: 0.0000 chunk 75 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6775 Z= 0.219 Angle : 0.471 6.408 9168 Z= 0.245 Chirality : 0.039 0.160 1103 Planarity : 0.004 0.044 1155 Dihedral : 3.796 20.301 916 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.54 % Allowed : 11.90 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.29), residues: 863 helix: 2.26 (0.24), residues: 475 sheet: -0.64 (0.51), residues: 92 loop : 0.16 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 736 HIS 0.001 0.001 HIS A 394 PHE 0.022 0.001 PHE A 702 TYR 0.014 0.001 TYR A 75 ARG 0.002 0.000 ARG A 760 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 100 time to evaluate : 0.805 Fit side-chains REVERT: A 25 LYS cc_start: 0.8054 (mmmt) cc_final: 0.7776 (mttm) REVERT: A 449 LYS cc_start: 0.8616 (mmtp) cc_final: 0.8188 (mmtm) REVERT: A 464 LYS cc_start: 0.8295 (mtmm) cc_final: 0.7691 (mtmm) REVERT: A 735 LEU cc_start: 0.8536 (mt) cc_final: 0.8202 (mt) REVERT: A 828 SER cc_start: 0.8372 (t) cc_final: 0.8134 (m) REVERT: A 853 MET cc_start: 0.7653 (mmm) cc_final: 0.7421 (mmm) outliers start: 19 outliers final: 15 residues processed: 110 average time/residue: 0.1898 time to fit residues: 28.0675 Evaluate side-chains 113 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 895 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 84 optimal weight: 0.2980 chunk 69 optimal weight: 0.9990 chunk 38 optimal weight: 0.0270 chunk 6 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6775 Z= 0.182 Angle : 0.460 6.740 9168 Z= 0.238 Chirality : 0.039 0.155 1103 Planarity : 0.004 0.045 1155 Dihedral : 3.716 20.091 916 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.54 % Allowed : 12.43 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.29), residues: 863 helix: 2.32 (0.24), residues: 475 sheet: -0.62 (0.51), residues: 92 loop : 0.19 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 460 HIS 0.001 0.000 HIS A 149 PHE 0.023 0.001 PHE A 702 TYR 0.014 0.001 TYR A 75 ARG 0.002 0.000 ARG A 760 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 103 time to evaluate : 0.794 Fit side-chains REVERT: A 25 LYS cc_start: 0.7983 (mmmt) cc_final: 0.7552 (mttm) REVERT: A 28 GLU cc_start: 0.6625 (mp0) cc_final: 0.6417 (mp0) REVERT: A 449 LYS cc_start: 0.8618 (mmtp) cc_final: 0.8232 (mmtm) REVERT: A 464 LYS cc_start: 0.8290 (mtmm) cc_final: 0.7664 (mtmm) REVERT: A 735 LEU cc_start: 0.8507 (mt) cc_final: 0.8168 (mt) REVERT: A 800 ASP cc_start: 0.6268 (t0) cc_final: 0.5961 (t0) REVERT: A 828 SER cc_start: 0.8368 (t) cc_final: 0.8142 (m) REVERT: A 853 MET cc_start: 0.7645 (mmm) cc_final: 0.7408 (mmm) outliers start: 19 outliers final: 12 residues processed: 111 average time/residue: 0.1951 time to fit residues: 28.9848 Evaluate side-chains 110 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 895 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 52 optimal weight: 0.0970 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6775 Z= 0.221 Angle : 0.480 6.802 9168 Z= 0.249 Chirality : 0.040 0.159 1103 Planarity : 0.004 0.046 1155 Dihedral : 3.783 20.267 916 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.54 % Allowed : 12.83 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.29), residues: 863 helix: 2.27 (0.24), residues: 475 sheet: -0.47 (0.57), residues: 77 loop : 0.23 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 460 HIS 0.001 0.001 HIS A 364 PHE 0.022 0.001 PHE A 702 TYR 0.014 0.001 TYR A 75 ARG 0.002 0.000 ARG A 760 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 102 time to evaluate : 0.731 Fit side-chains REVERT: A 25 LYS cc_start: 0.7957 (mmmt) cc_final: 0.7525 (mttm) REVERT: A 28 GLU cc_start: 0.6600 (mp0) cc_final: 0.6319 (mp0) REVERT: A 449 LYS cc_start: 0.8598 (mmtp) cc_final: 0.8216 (mmtm) REVERT: A 464 LYS cc_start: 0.8288 (mtmm) cc_final: 0.7900 (mtmt) REVERT: A 735 LEU cc_start: 0.8611 (mt) cc_final: 0.8293 (mt) REVERT: A 800 ASP cc_start: 0.6229 (t0) cc_final: 0.5976 (t0) REVERT: A 801 ASN cc_start: 0.8034 (OUTLIER) cc_final: 0.7828 (t0) REVERT: A 853 MET cc_start: 0.7658 (mmm) cc_final: 0.7418 (mmm) outliers start: 19 outliers final: 15 residues processed: 110 average time/residue: 0.2023 time to fit residues: 29.8238 Evaluate side-chains 114 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 98 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 895 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 57 optimal weight: 0.0470 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.6882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6775 Z= 0.232 Angle : 0.493 6.903 9168 Z= 0.255 Chirality : 0.040 0.160 1103 Planarity : 0.004 0.046 1155 Dihedral : 3.825 20.663 916 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.67 % Allowed : 13.64 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.29), residues: 863 helix: 2.24 (0.24), residues: 475 sheet: -0.50 (0.57), residues: 77 loop : 0.17 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 460 HIS 0.001 0.001 HIS A 364 PHE 0.022 0.001 PHE A 702 TYR 0.015 0.001 TYR A 75 ARG 0.002 0.000 ARG A 760 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 101 time to evaluate : 0.874 Fit side-chains REVERT: A 25 LYS cc_start: 0.7935 (mmmt) cc_final: 0.7288 (mtpp) REVERT: A 28 GLU cc_start: 0.6614 (mp0) cc_final: 0.6373 (mp0) REVERT: A 449 LYS cc_start: 0.8602 (mmtp) cc_final: 0.8224 (mmtm) REVERT: A 464 LYS cc_start: 0.8233 (mtmm) cc_final: 0.7585 (mtmm) REVERT: A 735 LEU cc_start: 0.8618 (mt) cc_final: 0.8301 (mt) REVERT: A 800 ASP cc_start: 0.6202 (t0) cc_final: 0.5969 (t0) REVERT: A 853 MET cc_start: 0.7712 (mmm) cc_final: 0.7471 (mmm) outliers start: 20 outliers final: 17 residues processed: 110 average time/residue: 0.1960 time to fit residues: 28.7819 Evaluate side-chains 115 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 98 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 895 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 57 optimal weight: 0.0060 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6775 Z= 0.209 Angle : 0.480 6.806 9168 Z= 0.250 Chirality : 0.039 0.156 1103 Planarity : 0.004 0.045 1155 Dihedral : 3.783 20.509 916 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.54 % Allowed : 14.17 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.29), residues: 863 helix: 2.23 (0.24), residues: 481 sheet: -0.46 (0.57), residues: 77 loop : 0.21 (0.37), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 460 HIS 0.001 0.000 HIS A 364 PHE 0.022 0.001 PHE A 702 TYR 0.014 0.001 TYR A 75 ARG 0.002 0.000 ARG A 760 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 103 time to evaluate : 0.691 Fit side-chains REVERT: A 25 LYS cc_start: 0.7909 (mmmt) cc_final: 0.7338 (mtpp) REVERT: A 28 GLU cc_start: 0.6749 (mp0) cc_final: 0.6545 (mp0) REVERT: A 449 LYS cc_start: 0.8599 (mmtp) cc_final: 0.8222 (mmtm) REVERT: A 464 LYS cc_start: 0.8238 (mtmm) cc_final: 0.7591 (mtmm) REVERT: A 735 LEU cc_start: 0.8534 (mt) cc_final: 0.8201 (mt) REVERT: A 800 ASP cc_start: 0.6130 (t0) cc_final: 0.5873 (t0) REVERT: A 853 MET cc_start: 0.7708 (mmm) cc_final: 0.7467 (mmm) outliers start: 19 outliers final: 18 residues processed: 111 average time/residue: 0.1974 time to fit residues: 29.3827 Evaluate side-chains 118 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 100 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 895 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 69 optimal weight: 0.2980 chunk 7 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 54 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 63 optimal weight: 0.3980 chunk 10 optimal weight: 6.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6775 Z= 0.217 Angle : 0.918 59.198 9168 Z= 0.533 Chirality : 0.040 0.156 1103 Planarity : 0.004 0.045 1155 Dihedral : 3.795 20.540 916 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.54 % Allowed : 14.17 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.29), residues: 863 helix: 2.24 (0.24), residues: 481 sheet: -0.46 (0.57), residues: 77 loop : 0.18 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 460 HIS 0.001 0.000 HIS A 364 PHE 0.022 0.001 PHE A 702 TYR 0.014 0.001 TYR A 75 ARG 0.002 0.000 ARG A 760 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 100 time to evaluate : 0.803 Fit side-chains REVERT: A 25 LYS cc_start: 0.7906 (mmmt) cc_final: 0.7333 (mtpp) REVERT: A 28 GLU cc_start: 0.6746 (mp0) cc_final: 0.6537 (mp0) REVERT: A 449 LYS cc_start: 0.8598 (mmtp) cc_final: 0.8221 (mmtm) REVERT: A 464 LYS cc_start: 0.8238 (mtmm) cc_final: 0.7588 (mtmm) REVERT: A 735 LEU cc_start: 0.8531 (mt) cc_final: 0.8198 (mt) REVERT: A 800 ASP cc_start: 0.6123 (t0) cc_final: 0.5592 (t0) REVERT: A 853 MET cc_start: 0.7707 (mmm) cc_final: 0.7468 (mmm) outliers start: 19 outliers final: 18 residues processed: 108 average time/residue: 0.1868 time to fit residues: 26.8940 Evaluate side-chains 118 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 100 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 895 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 2.9990 chunk 69 optimal weight: 0.2980 chunk 28 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.0470 chunk 60 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 79 optimal weight: 0.3980 chunk 46 optimal weight: 0.0030 overall best weight: 0.2688 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.162023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.134411 restraints weight = 7021.470| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.19 r_work: 0.3174 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6775 Z= 0.217 Angle : 0.918 59.198 9168 Z= 0.533 Chirality : 0.040 0.156 1103 Planarity : 0.004 0.045 1155 Dihedral : 3.795 20.540 916 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.41 % Allowed : 14.17 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.29), residues: 863 helix: 2.24 (0.24), residues: 481 sheet: -0.46 (0.57), residues: 77 loop : 0.18 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 460 HIS 0.001 0.000 HIS A 364 PHE 0.022 0.001 PHE A 702 TYR 0.014 0.001 TYR A 75 ARG 0.002 0.000 ARG A 760 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1746.92 seconds wall clock time: 32 minutes 33.60 seconds (1953.60 seconds total)