Starting phenix.real_space_refine on Tue Sep 24 08:01:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n75_24220/09_2024/7n75_24220.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n75_24220/09_2024/7n75_24220.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n75_24220/09_2024/7n75_24220.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n75_24220/09_2024/7n75_24220.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n75_24220/09_2024/7n75_24220.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n75_24220/09_2024/7n75_24220.cif" } resolution = 2.9 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= 0.001 sd= 0.022 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: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 4740 2.51 5 N 1272 2.21 5 O 1326 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 7381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1036, 7378 Classifications: {'peptide': 1036} Incomplete info: {'truncation_to_alanine': 184} Link IDs: {'PCIS': 3, 'PTRANS': 69, 'TRANS': 963} Chain breaks: 5 Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 668 Unresolved non-hydrogen angles: 855 Unresolved non-hydrogen dihedrals: 561 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 8, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 5, 'HIS:plan': 4, 'PHE:plan': 6, 'GLU:plan': 13, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 348 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 4.89, per 1000 atoms: 0.66 Number of scatterers: 7381 At special positions: 0 Unit cell: (92.312, 104.9, 127.978, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 1326 8.00 N 1272 7.00 C 4740 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 1.1 seconds 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1934 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 9 sheets defined 52.1% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 43 through 58 removed outlier: 4.228A pdb=" N ALA A 58 " --> pdb=" O VAL A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 68 Processing helix chain 'A' and resid 68 through 77 removed outlier: 4.119A pdb=" N GLY A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 85 Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 188 through 196 Processing helix chain 'A' and resid 200 through 212 Processing helix chain 'A' and resid 222 through 232 Processing helix chain 'A' and resid 233 through 249 Processing helix chain 'A' and resid 251 through 285 Processing helix chain 'A' and resid 305 through 307 No H-bonds generated for 'chain 'A' and resid 305 through 307' Processing helix chain 'A' and resid 364 through 366 No H-bonds generated for 'chain 'A' and resid 364 through 366' Processing helix chain 'A' and resid 393 through 396 Processing helix chain 'A' and resid 397 through 408 Processing helix chain 'A' and resid 419 through 445 removed outlier: 3.690A pdb=" N LEU A 430 " --> pdb=" O ALA A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 463 removed outlier: 3.967A pdb=" N VAL A 463 " --> pdb=" O LEU A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 487 removed outlier: 3.647A pdb=" N THR A 476 " --> pdb=" O MET A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 500 removed outlier: 3.800A pdb=" N ASN A 497 " --> pdb=" O LEU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 541 removed outlier: 3.941A pdb=" N ARG A 540 " --> pdb=" O GLU A 537 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 537 through 541' Processing helix chain 'A' and resid 544 through 553 Processing helix chain 'A' and resid 566 through 577 Processing helix chain 'A' and resid 651 through 659 Processing helix chain 'A' and resid 667 through 678 removed outlier: 3.516A pdb=" N ALA A 678 " --> pdb=" O SER A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 701 removed outlier: 3.722A pdb=" N GLN A 701 " --> pdb=" O GLU A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 709 Processing helix chain 'A' and resid 726 through 737 Processing helix chain 'A' and resid 748 through 759 Processing helix chain 'A' and resid 821 through 832 Processing helix chain 'A' and resid 835 through 842 Processing helix chain 'A' and resid 850 through 863 Processing helix chain 'A' and resid 877 through 884 Processing helix chain 'A' and resid 909 through 949 removed outlier: 3.672A pdb=" N ILE A 949 " --> pdb=" O ILE A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 964 Processing helix chain 'A' and resid 965 through 974 removed outlier: 4.104A pdb=" N SER A 974 " --> pdb=" O ALA A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1020 removed outlier: 3.900A pdb=" N ALA A1020 " --> pdb=" O PHE A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1061 removed outlier: 3.834A pdb=" N LEU A1054 " --> pdb=" O SER A1050 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A1061 " --> pdb=" O ALA A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1072 Processing helix chain 'A' and resid 1073 through 1093 Processing helix chain 'A' and resid 1109 through 1145 Proline residue: A1138 - end of helix Processing helix chain 'A' and resid 1152 through 1164 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 41 removed outlier: 3.930A pdb=" N ARG A 78 " --> pdb=" O CYS A 41 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 109 removed outlier: 5.316A pdb=" N ARG A 159 " --> pdb=" O TRP A 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 289 through 292 Processing sheet with id=AA5, first strand: chain 'A' and resid 312 through 315 removed outlier: 4.735A pdb=" N VAL A 386 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU A 387 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASP A 325 " --> pdb=" O THR A 391 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 346 through 350 removed outlier: 6.643A pdb=" N GLU A 332 " --> pdb=" O ALA A 378 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ALA A 378 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N MET A 334 " --> pdb=" O LEU A 376 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 488 through 490 removed outlier: 5.795A pdb=" N GLY A 887 " --> pdb=" O PHE A 901 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N SER A 903 " --> pdb=" O GLY A 887 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N SER A 889 " --> pdb=" O SER A 903 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N THR A 844 " --> pdb=" O ALA A 741 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR A 844 " --> pdb=" O ARG A 816 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LEU A 818 " --> pdb=" O THR A 844 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N PHE A 846 " --> pdb=" O LEU A 818 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU A 820 " --> pdb=" O PHE A 846 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU A 768 " --> pdb=" O MET A 789 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 519 through 525 removed outlier: 5.355A pdb=" N VAL A 520 " --> pdb=" O ARG A 720 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ARG A 720 " --> pdb=" O VAL A 520 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY A 522 " --> pdb=" O VAL A 718 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N LEU A 713 " --> pdb=" O SER A 687 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N SER A 687 " --> pdb=" O LEU A 713 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ARG A 631 " --> pdb=" O PHE A 625 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N PHE A 625 " --> pdb=" O ARG A 631 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ALA A 637 " --> pdb=" O VAL A 619 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N VAL A 619 " --> pdb=" O ALA A 637 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER A 588 " --> pdb=" O VAL A 619 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 579 " --> pdb=" O GLY A 591 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 557 through 559 removed outlier: 3.972A pdb=" N SER A 557 " --> pdb=" O VAL A 564 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A 564 " --> pdb=" O SER A 557 " (cutoff:3.500A) 461 hydrogen bonds defined for protein. 1323 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: 2.80 Time building geometry restraints manager: 2.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1397 1.33 - 1.45: 1697 1.45 - 1.57: 4361 1.57 - 1.69: 0 1.69 - 1.81: 63 Bond restraints: 7518 Sorted by residual: bond pdb=" CB VAL A 107 " pdb=" CG2 VAL A 107 " ideal model delta sigma weight residual 1.521 1.334 0.187 3.30e-02 9.18e+02 3.22e+01 bond pdb=" CB TYR A 935 " pdb=" CG TYR A 935 " ideal model delta sigma weight residual 1.512 1.410 0.102 2.20e-02 2.07e+03 2.15e+01 bond pdb=" CB VAL A 105 " pdb=" CG1 VAL A 105 " ideal model delta sigma weight residual 1.521 1.400 0.121 3.30e-02 9.18e+02 1.34e+01 bond pdb=" CE1 TYR A 935 " pdb=" CZ TYR A 935 " ideal model delta sigma weight residual 1.378 1.303 0.075 2.40e-02 1.74e+03 9.67e+00 bond pdb=" C TYR A 935 " pdb=" O TYR A 935 " ideal model delta sigma weight residual 1.236 1.205 0.031 1.21e-02 6.83e+03 6.44e+00 ... (remaining 7513 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 10135 2.36 - 4.73: 134 4.73 - 7.09: 11 7.09 - 9.45: 2 9.45 - 11.82: 1 Bond angle restraints: 10283 Sorted by residual: angle pdb=" CG1 VAL A 107 " pdb=" CB VAL A 107 " pdb=" CG2 VAL A 107 " ideal model delta sigma weight residual 110.80 98.98 11.82 2.20e+00 2.07e-01 2.89e+01 angle pdb=" N VAL A 897 " pdb=" CA VAL A 897 " pdb=" C VAL A 897 " ideal model delta sigma weight residual 113.20 108.75 4.45 9.60e-01 1.09e+00 2.15e+01 angle pdb=" C TYR A 935 " pdb=" N SER A 936 " pdb=" CA SER A 936 " ideal model delta sigma weight residual 120.44 124.73 -4.29 1.30e+00 5.92e-01 1.09e+01 angle pdb=" N PHE A 103 " pdb=" CA PHE A 103 " pdb=" C PHE A 103 " ideal model delta sigma weight residual 109.50 105.20 4.30 1.58e+00 4.01e-01 7.39e+00 angle pdb=" CA VAL A 107 " pdb=" CB VAL A 107 " pdb=" CG2 VAL A 107 " ideal model delta sigma weight residual 110.40 105.90 4.50 1.70e+00 3.46e-01 7.01e+00 ... (remaining 10278 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 4155 17.88 - 35.77: 284 35.77 - 53.65: 35 53.65 - 71.53: 9 71.53 - 89.42: 7 Dihedral angle restraints: 4490 sinusoidal: 1497 harmonic: 2993 Sorted by residual: dihedral pdb=" CA SER A 889 " pdb=" C SER A 889 " pdb=" N LEU A 890 " pdb=" CA LEU A 890 " ideal model delta harmonic sigma weight residual 180.00 -162.71 -17.29 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA CYS A1136 " pdb=" C CYS A1136 " pdb=" N LEU A1137 " pdb=" CA LEU A1137 " ideal model delta harmonic sigma weight residual -180.00 -162.90 -17.10 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA GLN A 865 " pdb=" C GLN A 865 " pdb=" N TYR A 866 " pdb=" CA TYR A 866 " ideal model delta harmonic sigma weight residual 180.00 163.02 16.98 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 4487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1160 0.083 - 0.166: 103 0.166 - 0.249: 2 0.249 - 0.332: 0 0.332 - 0.415: 1 Chirality restraints: 1266 Sorted by residual: chirality pdb=" CG LEU A 158 " pdb=" CB LEU A 158 " pdb=" CD1 LEU A 158 " pdb=" CD2 LEU A 158 " both_signs ideal model delta sigma weight residual False -2.59 -2.17 -0.41 2.00e-01 2.50e+01 4.30e+00 chirality pdb=" CB VAL A 969 " pdb=" CA VAL A 969 " pdb=" CG1 VAL A 969 " pdb=" CG2 VAL A 969 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB ILE A 441 " pdb=" CA ILE A 441 " pdb=" CG1 ILE A 441 " pdb=" CG2 ILE A 441 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.05e-01 ... (remaining 1263 not shown) Planarity restraints: 1314 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 935 " 0.066 2.00e-02 2.50e+03 3.55e-02 2.52e+01 pdb=" CG TYR A 935 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TYR A 935 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR A 935 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR A 935 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 935 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 935 " 0.024 2.00e-02 2.50e+03 pdb=" OH TYR A 935 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 955 " -0.015 2.00e-02 2.50e+03 3.14e-02 9.83e+00 pdb=" CG ASP A 955 " 0.054 2.00e-02 2.50e+03 pdb=" OD1 ASP A 955 " -0.020 2.00e-02 2.50e+03 pdb=" OD2 ASP A 955 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 934 " -0.015 2.00e-02 2.50e+03 3.08e-02 9.48e+00 pdb=" C LEU A 934 " 0.053 2.00e-02 2.50e+03 pdb=" O LEU A 934 " -0.020 2.00e-02 2.50e+03 pdb=" N TYR A 935 " -0.018 2.00e-02 2.50e+03 ... (remaining 1311 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 184 2.71 - 3.25: 7513 3.25 - 3.80: 12082 3.80 - 4.35: 14712 4.35 - 4.90: 25727 Nonbonded interactions: 60218 Sorted by model distance: nonbonded pdb=" OH TYR A 235 " pdb=" O PRO A 465 " model vdw 2.157 3.040 nonbonded pdb=" OH TYR A 359 " pdb=" OG1 THR A 368 " model vdw 2.202 3.040 nonbonded pdb=" OG SER A 889 " pdb=" OG SER A 899 " model vdw 2.227 3.040 nonbonded pdb=" O ASP A 325 " pdb=" OG1 THR A 391 " model vdw 2.254 3.040 nonbonded pdb=" OE2 GLU A 860 " pdb=" NZ LYS A 863 " model vdw 2.273 3.120 ... (remaining 60213 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.470 Find NCS groups from input model: 0.070 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:10.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 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 : 0.007 0.187 7518 Z= 0.416 Angle : 0.689 11.817 10283 Z= 0.376 Chirality : 0.047 0.415 1266 Planarity : 0.005 0.058 1314 Dihedral : 12.885 89.418 2556 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.26), residues: 1024 helix: 1.13 (0.23), residues: 496 sheet: 0.16 (0.39), residues: 161 loop : -0.04 (0.35), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 100 HIS 0.002 0.001 HIS A 367 PHE 0.041 0.002 PHE A 958 TYR 0.066 0.003 TYR A 935 ARG 0.006 0.001 ARG A1153 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.814 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 1.0279 time to fit residues: 56.7270 Evaluate side-chains 36 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 43 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 52 optimal weight: 50.0000 chunk 41 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 49 optimal weight: 40.0000 chunk 60 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN A1042 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7518 Z= 0.215 Angle : 0.560 7.309 10283 Z= 0.284 Chirality : 0.041 0.142 1266 Planarity : 0.005 0.054 1314 Dihedral : 4.219 16.078 1097 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.85 % Allowed : 5.55 % Favored : 93.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 1.42 (0.27), residues: 1024 helix: 1.74 (0.23), residues: 508 sheet: 0.41 (0.42), residues: 160 loop : 0.15 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 170 HIS 0.002 0.001 HIS A 408 PHE 0.022 0.001 PHE A 958 TYR 0.018 0.001 TYR A 935 ARG 0.010 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.842 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 43 average time/residue: 1.1615 time to fit residues: 53.8182 Evaluate side-chains 40 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 905 MET Chi-restraints excluded: chain A residue 981 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 40.0000 chunk 29 optimal weight: 10.0000 chunk 77 optimal weight: 0.0970 chunk 63 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 93 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7518 Z= 0.178 Angle : 0.520 7.096 10283 Z= 0.258 Chirality : 0.040 0.132 1266 Planarity : 0.004 0.046 1314 Dihedral : 3.899 15.861 1097 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.85 % Allowed : 8.11 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 1.83 (0.27), residues: 1024 helix: 2.14 (0.23), residues: 510 sheet: 0.45 (0.42), residues: 162 loop : 0.31 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 170 HIS 0.002 0.001 HIS A 775 PHE 0.017 0.001 PHE A 958 TYR 0.015 0.001 TYR A 935 ARG 0.008 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.719 Fit side-chains REVERT: A 894 GLU cc_start: 0.6702 (tp30) cc_final: 0.6463 (tp30) outliers start: 6 outliers final: 0 residues processed: 47 average time/residue: 1.0400 time to fit residues: 53.1294 Evaluate side-chains 38 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 92 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 48 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 44 optimal weight: 40.0000 chunk 62 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 49 optimal weight: 50.0000 chunk 89 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7518 Z= 0.207 Angle : 0.527 6.991 10283 Z= 0.258 Chirality : 0.041 0.136 1266 Planarity : 0.004 0.048 1314 Dihedral : 3.853 17.611 1097 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.00 % Allowed : 10.38 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 2.02 (0.27), residues: 1024 helix: 2.31 (0.23), residues: 511 sheet: 0.45 (0.41), residues: 162 loop : 0.41 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 170 HIS 0.001 0.000 HIS A 775 PHE 0.014 0.001 PHE A 958 TYR 0.013 0.001 TYR A 935 ARG 0.012 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 40 time to evaluate : 0.911 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 43 average time/residue: 1.0414 time to fit residues: 48.7480 Evaluate side-chains 39 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 973 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 1 optimal weight: 20.0000 chunk 74 optimal weight: 0.3980 chunk 41 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 50.0000 chunk 89 optimal weight: 6.9990 chunk 25 optimal weight: 0.4980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7518 Z= 0.205 Angle : 0.525 7.220 10283 Z= 0.257 Chirality : 0.040 0.134 1266 Planarity : 0.004 0.062 1314 Dihedral : 3.774 15.893 1097 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.85 % Allowed : 11.52 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 2.15 (0.27), residues: 1024 helix: 2.46 (0.22), residues: 510 sheet: 0.45 (0.42), residues: 151 loop : 0.46 (0.35), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 170 HIS 0.001 0.000 HIS A 775 PHE 0.014 0.001 PHE A 940 TYR 0.013 0.001 TYR A 935 ARG 0.012 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.887 Fit side-chains REVERT: A 894 GLU cc_start: 0.6610 (tp30) cc_final: 0.6355 (tp30) outliers start: 6 outliers final: 2 residues processed: 39 average time/residue: 1.1138 time to fit residues: 46.9765 Evaluate side-chains 38 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 973 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 19 optimal weight: 0.8980 chunk 58 optimal weight: 50.0000 chunk 24 optimal weight: 7.9990 chunk 99 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 46 optimal weight: 40.0000 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 0.0470 chunk 52 optimal weight: 50.0000 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7518 Z= 0.199 Angle : 0.520 7.443 10283 Z= 0.253 Chirality : 0.040 0.134 1266 Planarity : 0.004 0.064 1314 Dihedral : 3.712 16.020 1097 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.14 % Allowed : 12.38 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 2.19 (0.27), residues: 1024 helix: 2.53 (0.22), residues: 511 sheet: 0.34 (0.42), residues: 150 loop : 0.46 (0.35), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 170 HIS 0.001 0.000 HIS A 367 PHE 0.013 0.001 PHE A 940 TYR 0.012 0.001 TYR A 935 ARG 0.016 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 36 time to evaluate : 0.936 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 40 average time/residue: 1.0255 time to fit residues: 44.7555 Evaluate side-chains 39 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 973 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 55 optimal weight: 30.0000 chunk 99 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 45 optimal weight: 40.0000 chunk 61 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7518 Z= 0.222 Angle : 0.543 8.176 10283 Z= 0.261 Chirality : 0.040 0.138 1266 Planarity : 0.004 0.063 1314 Dihedral : 3.704 16.008 1097 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.14 % Allowed : 12.94 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 2.22 (0.27), residues: 1024 helix: 2.58 (0.22), residues: 511 sheet: 0.25 (0.41), residues: 152 loop : 0.50 (0.35), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 246 HIS 0.001 0.000 HIS A 817 PHE 0.013 0.001 PHE A 940 TYR 0.011 0.001 TYR A 935 ARG 0.013 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 37 time to evaluate : 0.838 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 42 average time/residue: 1.0394 time to fit residues: 47.4864 Evaluate side-chains 41 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 973 MET Chi-restraints excluded: chain A residue 981 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 0.9990 chunk 59 optimal weight: 50.0000 chunk 29 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 49 optimal weight: 50.0000 chunk 9 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 90 optimal weight: 0.0980 chunk 95 optimal weight: 0.9980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 939 GLN A 962 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7518 Z= 0.174 Angle : 0.530 8.996 10283 Z= 0.253 Chirality : 0.040 0.138 1266 Planarity : 0.004 0.076 1314 Dihedral : 3.625 15.956 1097 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.42 % Allowed : 12.80 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 2.34 (0.27), residues: 1024 helix: 2.69 (0.23), residues: 511 sheet: 0.36 (0.42), residues: 144 loop : 0.49 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 170 HIS 0.001 0.000 HIS A 775 PHE 0.013 0.001 PHE A 940 TYR 0.012 0.001 TYR A 935 ARG 0.017 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 38 time to evaluate : 0.837 Fit side-chains revert: symmetry clash REVERT: A 894 GLU cc_start: 0.6434 (tp30) cc_final: 0.6186 (tp30) outliers start: 10 outliers final: 3 residues processed: 44 average time/residue: 0.8952 time to fit residues: 43.1756 Evaluate side-chains 38 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 432 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 55 optimal weight: 50.0000 chunk 40 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 60 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7518 Z= 0.190 Angle : 0.549 9.282 10283 Z= 0.260 Chirality : 0.040 0.137 1266 Planarity : 0.004 0.067 1314 Dihedral : 3.609 15.931 1097 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.71 % Allowed : 13.94 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 2.37 (0.27), residues: 1024 helix: 2.71 (0.22), residues: 512 sheet: 0.42 (0.42), residues: 144 loop : 0.50 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 170 HIS 0.001 0.000 HIS A 367 PHE 0.012 0.001 PHE A 940 TYR 0.014 0.001 TYR A 935 ARG 0.016 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 35 time to evaluate : 0.835 Fit side-chains REVERT: A 894 GLU cc_start: 0.6305 (tp30) cc_final: 0.6092 (tp30) outliers start: 5 outliers final: 3 residues processed: 39 average time/residue: 1.0150 time to fit residues: 43.3294 Evaluate side-chains 38 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 432 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 50.0000 chunk 46 optimal weight: 50.0000 chunk 68 optimal weight: 0.9980 chunk 102 optimal weight: 0.0770 chunk 94 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 50.0000 chunk 64 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7518 Z= 0.171 Angle : 0.547 9.807 10283 Z= 0.259 Chirality : 0.040 0.135 1266 Planarity : 0.004 0.091 1314 Dihedral : 3.620 16.770 1097 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.43 % Allowed : 14.22 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 2.38 (0.27), residues: 1024 helix: 2.73 (0.22), residues: 512 sheet: 0.42 (0.42), residues: 144 loop : 0.49 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 170 HIS 0.001 0.000 HIS A 775 PHE 0.013 0.001 PHE A 940 TYR 0.019 0.001 TYR A 935 ARG 0.020 0.000 ARG A 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 0.848 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 40 average time/residue: 1.0943 time to fit residues: 47.4943 Evaluate side-chains 37 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 386 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 34 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 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 = 0.3783 r_free = 0.3783 target = 0.093601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.063766 restraints weight = 19677.804| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.09 r_work: 0.2952 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7518 Z= 0.198 Angle : 0.560 9.809 10283 Z= 0.265 Chirality : 0.040 0.140 1266 Planarity : 0.004 0.086 1314 Dihedral : 3.598 15.936 1097 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.00 % Allowed : 13.66 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 2.40 (0.27), residues: 1024 helix: 2.74 (0.22), residues: 512 sheet: 0.39 (0.42), residues: 144 loop : 0.51 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 246 HIS 0.001 0.000 HIS A 817 PHE 0.013 0.001 PHE A 940 TYR 0.019 0.001 TYR A 935 ARG 0.020 0.000 ARG A 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1982.16 seconds wall clock time: 35 minutes 47.91 seconds (2147.91 seconds total)