Starting phenix.real_space_refine on Tue Feb 13 19:04:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n75_24220/02_2024/7n75_24220.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n75_24220/02_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_24220/02_2024/7n75_24220.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n75_24220/02_2024/7n75_24220.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n75_24220/02_2024/7n75_24220.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n75_24220/02_2024/7n75_24220.pdb" } 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 Residue "A PHE 1154": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7381 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1039, 7381 Classifications: {'peptide': 1036, 'water': 3} Incomplete info: {'truncation_to_alanine': 184} Link IDs: {'PCIS': 3, 'PTRANS': 69, 'TRANS': 963, None: 3} Not linked: pdbres="PRO A1168 " pdbres="HOH A1201 " Not linked: pdbres="HOH A1201 " pdbres="HOH A1202 " Not linked: pdbres="HOH A1202 " pdbres="HOH A1203 " 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 Time building chain proxies: 4.49, per 1000 atoms: 0.61 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.85 Conformation dependent library (CDL) restraints added in 1.5 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: 1.18 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: 3.02 Time building geometry restraints manager: 3.09 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: 97.23 - 104.60: 179 104.60 - 111.96: 3886 111.96 - 119.32: 2260 119.32 - 126.68: 3862 126.68 - 134.04: 96 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 2.440 nonbonded pdb=" OH TYR A 359 " pdb=" OG1 THR A 368 " model vdw 2.202 2.440 nonbonded pdb=" OG SER A 889 " pdb=" OG SER A 899 " model vdw 2.227 2.440 nonbonded pdb=" O ASP A 325 " pdb=" OG1 THR A 391 " model vdw 2.254 2.440 nonbonded pdb=" OE2 GLU A 860 " pdb=" NZ LYS A 863 " model vdw 2.273 2.520 ... (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: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 5.850 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 25.220 Find NCS groups from input model: 0.230 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:10.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.230 ------------------------------------------------------------------------------- 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 : 0.783 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 1.0429 time to fit residues: 57.3953 Evaluate side-chains 36 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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: 0.1980 chunk 78 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 52 optimal weight: 50.0000 chunk 41 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 30.0000 chunk 60 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1120 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= 0.206 Angle : 0.545 7.214 10283 Z= 0.277 Chirality : 0.041 0.139 1266 Planarity : 0.005 0.055 1314 Dihedral : 4.174 16.319 1097 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.85 % Allowed : 4.98 % Favored : 94.17 % 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: 1.51 (0.27), residues: 1024 helix: 1.80 (0.23), residues: 508 sheet: 0.49 (0.42), residues: 155 loop : 0.20 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 170 HIS 0.002 0.001 HIS A 367 PHE 0.020 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 48 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.915 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 44 average time/residue: 1.1014 time to fit residues: 52.3018 Evaluate side-chains 36 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 905 MET 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: 0.9990 chunk 77 optimal weight: 0.4980 chunk 63 optimal weight: 0.9980 chunk 25 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 92 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 962 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: 0.1509 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= 0.183 Angle : 0.516 6.859 10283 Z= 0.255 Chirality : 0.040 0.133 1266 Planarity : 0.004 0.046 1314 Dihedral : 3.858 16.486 1097 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.85 % Allowed : 8.53 % Favored : 90.61 % 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: 1.92 (0.27), residues: 1024 helix: 2.21 (0.23), residues: 510 sheet: 0.48 (0.41), residues: 161 loop : 0.37 (0.35), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 170 HIS 0.002 0.000 HIS A 775 PHE 0.017 0.001 PHE A 958 TYR 0.014 0.001 TYR A 935 ARG 0.002 0.000 ARG A 740 *********************** 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 46 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 40 time to evaluate : 0.855 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 44 average time/residue: 1.0736 time to fit residues: 51.1891 Evaluate side-chains 38 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 92 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 44 optimal weight: 40.0000 chunk 62 optimal weight: 0.0770 chunk 94 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 892 GLN ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 7518 Z= 0.325 Angle : 0.572 7.439 10283 Z= 0.281 Chirality : 0.042 0.137 1266 Planarity : 0.004 0.045 1314 Dihedral : 3.925 15.936 1097 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.56 % Allowed : 10.10 % Favored : 88.34 % 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: 1.99 (0.27), residues: 1024 helix: 2.26 (0.23), residues: 510 sheet: 0.44 (0.41), residues: 160 loop : 0.45 (0.36), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1166 HIS 0.003 0.001 HIS A 367 PHE 0.016 0.002 PHE A1154 TYR 0.013 0.001 TYR A 935 ARG 0.006 0.000 ARG A 281 *********************** 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 46 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 35 time to evaluate : 0.836 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 42 average time/residue: 1.0499 time to fit residues: 47.8659 Evaluate side-chains 39 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 34 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 460 VAL Chi-restraints excluded: chain A residue 973 MET Chi-restraints excluded: chain A residue 981 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 1 optimal weight: 30.0000 chunk 74 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 50.0000 chunk 89 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 892 GLN ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7518 Z= 0.219 Angle : 0.523 7.215 10283 Z= 0.256 Chirality : 0.040 0.147 1266 Planarity : 0.004 0.045 1314 Dihedral : 3.796 15.614 1097 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.85 % Allowed : 11.66 % Favored : 87.48 % 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: 2.14 (0.27), residues: 1024 helix: 2.43 (0.23), residues: 510 sheet: 0.25 (0.40), residues: 168 loop : 0.62 (0.36), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1166 HIS 0.002 0.000 HIS A 367 PHE 0.014 0.001 PHE A 940 TYR 0.016 0.001 TYR A 935 ARG 0.003 0.000 ARG A 281 *********************** 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 48 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.822 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 45 average time/residue: 0.9977 time to fit residues: 48.7023 Evaluate side-chains 37 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.848 ------------------------------------------------------------------------------- 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: 0.7980 chunk 89 optimal weight: 0.0270 chunk 19 optimal weight: 5.9990 chunk 58 optimal weight: 50.0000 chunk 24 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 46 optimal weight: 40.0000 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 9.9990 chunk 52 optimal weight: 40.0000 overall best weight: 1.1642 ------------------------------------------------------------------------------- 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: 0.8039 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7518 Z= 0.233 Angle : 0.537 7.442 10283 Z= 0.261 Chirality : 0.040 0.137 1266 Planarity : 0.004 0.044 1314 Dihedral : 3.735 15.508 1097 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.28 % Allowed : 12.80 % 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: 2.53 (0.22), residues: 510 sheet: 0.16 (0.40), residues: 168 loop : 0.66 (0.36), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1166 HIS 0.002 0.000 HIS A 367 PHE 0.014 0.001 PHE A 940 TYR 0.017 0.001 TYR A 935 ARG 0.002 0.000 ARG A 281 *********************** 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: 9 poor density : 35 time to evaluate : 0.909 Fit side-chains REVERT: A 894 GLU cc_start: 0.6541 (tp30) cc_final: 0.6334 (tp30) outliers start: 9 outliers final: 4 residues processed: 39 average time/residue: 0.9833 time to fit residues: 42.0456 Evaluate side-chains 39 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 981 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 1.9990 chunk 11 optimal weight: 0.2980 chunk 56 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 55 optimal weight: 40.0000 chunk 99 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 45 optimal weight: 40.0000 chunk 61 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.2000 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= 0.182 Angle : 0.519 7.876 10283 Z= 0.251 Chirality : 0.040 0.136 1266 Planarity : 0.004 0.043 1314 Dihedral : 3.650 15.679 1097 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.71 % Allowed : 13.09 % Favored : 85.21 % 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: 2.32 (0.27), residues: 1024 helix: 2.65 (0.22), residues: 511 sheet: 0.38 (0.40), residues: 159 loop : 0.51 (0.36), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 170 HIS 0.002 0.000 HIS A 367 PHE 0.013 0.001 PHE A 940 TYR 0.018 0.001 TYR A 935 ARG 0.002 0.000 ARG A 740 *********************** 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 48 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 36 time to evaluate : 0.797 Fit side-chains outliers start: 12 outliers final: 4 residues processed: 44 average time/residue: 1.0131 time to fit residues: 48.5155 Evaluate side-chains 39 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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 935 TYR Chi-restraints excluded: chain A residue 973 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 0.7980 chunk 59 optimal weight: 50.0000 chunk 29 optimal weight: 0.1980 chunk 19 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 49 optimal weight: 40.0000 chunk 9 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 90 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.8009 moved from start: 0.2118 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= 0.171 Angle : 0.532 8.983 10283 Z= 0.256 Chirality : 0.040 0.135 1266 Planarity : 0.004 0.043 1314 Dihedral : 3.591 15.592 1097 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.42 % Allowed : 13.66 % Favored : 84.92 % 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: 2.40 (0.27), residues: 1024 helix: 2.74 (0.23), residues: 511 sheet: 0.41 (0.40), residues: 159 loop : 0.53 (0.36), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 170 HIS 0.002 0.000 HIS A 367 PHE 0.013 0.001 PHE A 940 TYR 0.020 0.001 TYR A 935 ARG 0.004 0.000 ARG A1159 *********************** 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 : 0.896 Fit side-chains REVERT: A 288 MET cc_start: 0.6955 (OUTLIER) cc_final: 0.6607 (ptp) outliers start: 10 outliers final: 5 residues processed: 44 average time/residue: 1.0438 time to fit residues: 50.3279 Evaluate side-chains 40 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 34 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 LEU 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 722 LEU Chi-restraints excluded: chain A residue 973 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 55 optimal weight: 50.0000 chunk 40 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2192 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= 0.182 Angle : 0.545 9.393 10283 Z= 0.261 Chirality : 0.040 0.135 1266 Planarity : 0.004 0.042 1314 Dihedral : 3.584 15.628 1097 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.28 % Allowed : 13.94 % Favored : 84.78 % 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: 2.44 (0.27), residues: 1024 helix: 2.86 (0.23), residues: 506 sheet: 0.28 (0.39), residues: 171 loop : 0.52 (0.36), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 170 HIS 0.001 0.000 HIS A 367 PHE 0.013 0.001 PHE A 940 TYR 0.023 0.001 TYR A 935 ARG 0.002 0.000 ARG A 740 *********************** 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 43 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 34 time to evaluate : 0.838 Fit side-chains REVERT: A 288 MET cc_start: 0.6996 (OUTLIER) cc_final: 0.6702 (ptp) outliers start: 9 outliers final: 6 residues processed: 39 average time/residue: 0.9112 time to fit residues: 39.1328 Evaluate side-chains 41 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 34 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 LEU 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 722 LEU Chi-restraints excluded: chain A residue 896 SER Chi-restraints excluded: chain A residue 973 MET 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: 40.0000 chunk 68 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 50 optimal weight: 50.0000 chunk 64 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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: 0.8020 moved from start: 0.2224 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= 0.206 Angle : 0.572 9.836 10283 Z= 0.270 Chirality : 0.040 0.136 1266 Planarity : 0.004 0.042 1314 Dihedral : 3.578 15.681 1097 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.00 % Allowed : 14.22 % Favored : 84.78 % 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: 2.43 (0.27), residues: 1024 helix: 2.75 (0.23), residues: 512 sheet: 0.30 (0.40), residues: 161 loop : 0.63 (0.36), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 246 HIS 0.002 0.000 HIS A 367 PHE 0.013 0.001 PHE A 940 TYR 0.022 0.001 TYR A 935 ARG 0.002 0.000 ARG A 740 ********************** 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 41 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 34 time to evaluate : 0.930 Fit side-chains REVERT: A 288 MET cc_start: 0.7037 (OUTLIER) cc_final: 0.6761 (ptp) outliers start: 7 outliers final: 4 residues processed: 38 average time/residue: 0.9382 time to fit residues: 39.1783 Evaluate side-chains 39 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 34 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 973 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 8.9990 chunk 75 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 22 optimal weight: 20.0000 chunk 81 optimal weight: 0.7980 chunk 34 optimal weight: 10.0000 chunk 84 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3788 r_free = 0.3788 target = 0.093890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.064301 restraints weight = 19679.849| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.09 r_work: 0.2956 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7518 Z= 0.189 Angle : 0.549 9.850 10283 Z= 0.262 Chirality : 0.040 0.135 1266 Planarity : 0.004 0.042 1314 Dihedral : 3.550 15.684 1097 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.14 % Allowed : 13.94 % Favored : 84.92 % 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: 2.50 (0.27), residues: 1024 helix: 2.82 (0.23), residues: 512 sheet: 0.32 (0.40), residues: 161 loop : 0.62 (0.36), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 170 HIS 0.002 0.000 HIS A 367 PHE 0.013 0.001 PHE A 940 TYR 0.021 0.001 TYR A 935 ARG 0.002 0.000 ARG A 740 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1980.66 seconds wall clock time: 36 minutes 18.68 seconds (2178.68 seconds total)