Starting phenix.real_space_refine on Tue Feb 11 18:24:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h3u_32828/02_2025/8h3u_32828.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h3u_32828/02_2025/8h3u_32828.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h3u_32828/02_2025/8h3u_32828.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h3u_32828/02_2025/8h3u_32828.map" model { file = "/net/cci-nas-00/data/ceres_data/8h3u_32828/02_2025/8h3u_32828.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h3u_32828/02_2025/8h3u_32828.cif" } resolution = 4.7 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= 0.020 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 44 5.16 5 C 4023 2.51 5 N 1076 2.21 5 O 1240 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-5592/modules/chem_data/mon_lib" Total number of atoms: 6383 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4539 Classifications: {'peptide': 583} Link IDs: {'PTRANS': 28, 'TRANS': 554} Chain breaks: 1 Chain: "B" Number of atoms: 1844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1844 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 220} Time building chain proxies: 4.44, per 1000 atoms: 0.70 Number of scatterers: 6383 At special positions: 0 Unit cell: (94.14, 94.14, 154.808, 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 44 16.00 O 1240 8.00 N 1076 7.00 C 4023 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 197 " distance=2.03 Simple disulfide: pdb=" SG CYS A 191 " - pdb=" SG CYS A 210 " distance=2.03 Simple disulfide: pdb=" SG CYS A 204 " - pdb=" SG CYS A 221 " distance=2.03 Simple disulfide: pdb=" SG CYS A 225 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 347 " - pdb=" SG CYS A 354 " distance=2.03 Simple disulfide: pdb=" SG CYS A 422 " - pdb=" SG CYS A 502 " distance=2.03 Simple disulfide: pdb=" SG CYS A 650 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 677 " distance=2.03 Simple disulfide: pdb=" SG CYS A 716 " - pdb=" SG CYS A 767 " distance=2.03 Simple disulfide: pdb=" SG CYS A 772 " - pdb=" SG CYS B 896 " distance=2.03 Simple disulfide: pdb=" SG CYS B 810 " - pdb=" SG CYS B 826 " distance=2.03 Simple disulfide: pdb=" SG CYS B 910 " - pdb=" SG CYS B 977 " distance=2.03 Simple disulfide: pdb=" SG CYS B 941 " - pdb=" SG CYS B 956 " distance=2.03 Simple disulfide: pdb=" SG CYS B 967 " - pdb=" SG CYS B 995 " distance=2.03 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: 1.72 Conformation dependent library (CDL) restraints added in 1.7 seconds 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1496 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 13 sheets defined 8.1% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 201 through 203 No H-bonds generated for 'chain 'A' and resid 201 through 203' Processing helix chain 'A' and resid 213 through 217 Processing helix chain 'A' and resid 286 through 290 removed outlier: 3.762A pdb=" N SER A 289 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS A 290 " --> pdb=" O GLY A 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 286 through 290' Processing helix chain 'A' and resid 340 through 346 Processing helix chain 'A' and resid 531 through 534 Processing helix chain 'A' and resid 671 through 675 Processing helix chain 'A' and resid 708 through 719 Processing helix chain 'B' and resid 833 through 835 No H-bonds generated for 'chain 'B' and resid 833 through 835' Processing helix chain 'B' and resid 937 through 945 Processing helix chain 'B' and resid 1007 through 1009 No H-bonds generated for 'chain 'B' and resid 1007 through 1009' Processing helix chain 'B' and resid 1010 through 1019 removed outlier: 3.965A pdb=" N PHE B1017 " --> pdb=" O TRP B1013 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N HIS B1019 " --> pdb=" O GLN B1015 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 190 removed outlier: 3.732A pdb=" N ILE A 198 " --> pdb=" O SER A 189 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 230 through 231 removed outlier: 6.433A pdb=" N LEU A 280 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N SER A 295 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ILE A 282 " --> pdb=" O ARG A 293 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 235 through 239 removed outlier: 3.537A pdb=" N GLY A 236 " --> pdb=" O TYR A 331 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N GLY A 326 " --> pdb=" O PHE A 272 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N PHE A 272 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASN A 328 " --> pdb=" O ASP A 270 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 357 through 358 Processing sheet with id=AA5, first strand: chain 'A' and resid 367 through 370 removed outlier: 3.704A pdb=" N ILE A 369 " --> pdb=" O TYR A 393 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TYR A 393 " --> pdb=" O ILE A 369 " (cutoff:3.500A) removed outlier: 12.752A pdb=" N PHE A 392 " --> pdb=" O ASP A 494 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ASP A 494 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 394 " --> pdb=" O LEU A 492 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N LEU A 492 " --> pdb=" O HIS A 428 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N HIS A 428 " --> pdb=" O LEU A 492 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ASP A 494 " --> pdb=" O TRP A 426 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TRP A 426 " --> pdb=" O ASP A 494 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 405 through 407 removed outlier: 3.521A pdb=" N SER A 438 " --> pdb=" O ASN A 480 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE A 482 " --> pdb=" O LYS A 436 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LYS A 436 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE A 452 " --> pdb=" O ILE A 439 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ILE A 441 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N THR A 450 " --> pdb=" O ILE A 441 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 536 through 537 removed outlier: 3.696A pdb=" N PHE A 537 " --> pdb=" O ALA A 629 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA A 629 " --> pdb=" O PHE A 537 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN A 630 " --> pdb=" O PHE A 568 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N PHE A 568 " --> pdb=" O ASN A 630 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N THR A 632 " --> pdb=" O LEU A 566 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N LEU A 566 " --> pdb=" O THR A 632 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 594 through 596 removed outlier: 3.695A pdb=" N ALA A 594 " --> pdb=" O ILE A 582 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 693 through 694 Processing sheet with id=AB1, first strand: chain 'A' and resid 724 through 729 removed outlier: 3.631A pdb=" N GLN A 766 " --> pdb=" O SER A 726 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS A 728 " --> pdb=" O ARG A 764 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 740 through 743 removed outlier: 3.570A pdb=" N THR A 752 " --> pdb=" O LYS A 740 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 789 through 790 removed outlier: 3.687A pdb=" N SER B 789 " --> pdb=" O GLU B 930 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLN B 929 " --> pdb=" O GLY B 914 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY B 914 " --> pdb=" O GLN B 929 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALA B 913 " --> pdb=" O PRO B 974 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY B 987 " --> pdb=" O LEU B 975 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N CYS B 977 " --> pdb=" O LEU B 985 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU B 985 " --> pdb=" O CYS B 977 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N VAL B1003 " --> pdb=" O SER B 990 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 808 through 812 removed outlier: 6.242A pdb=" N LEU B 808 " --> pdb=" O TYR B 804 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR B 804 " --> pdb=" O LEU B 808 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N CYS B 810 " --> pdb=" O LEU B 802 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU B 802 " --> pdb=" O CYS B 810 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL B 800 " --> pdb=" O ALA B 812 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N TRP B 837 " --> pdb=" O ILE B 859 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU B 861 " --> pdb=" O HIS B 881 " (cutoff:3.500A) 132 hydrogen bonds defined for protein. 336 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: 2.57 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2125 1.34 - 1.46: 1508 1.46 - 1.58: 2856 1.58 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 6543 Sorted by residual: bond pdb=" C PHE A 542 " pdb=" N PRO A 543 " ideal model delta sigma weight residual 1.337 1.356 -0.019 1.06e-02 8.90e+03 3.24e+00 bond pdb=" N PHE A 542 " pdb=" CA PHE A 542 " ideal model delta sigma weight residual 1.457 1.481 -0.024 1.41e-02 5.03e+03 2.95e+00 bond pdb=" N ASN A 541 " pdb=" CA ASN A 541 " ideal model delta sigma weight residual 1.466 1.487 -0.021 1.51e-02 4.39e+03 1.93e+00 bond pdb=" N ILE B 840 " pdb=" CA ILE B 840 " ideal model delta sigma weight residual 1.459 1.474 -0.015 1.19e-02 7.06e+03 1.62e+00 bond pdb=" N ILE A 750 " pdb=" CA ILE A 750 " ideal model delta sigma weight residual 1.459 1.474 -0.015 1.19e-02 7.06e+03 1.52e+00 ... (remaining 6538 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 8710 1.61 - 3.21: 177 3.21 - 4.82: 12 4.82 - 6.42: 3 6.42 - 8.03: 2 Bond angle restraints: 8904 Sorted by residual: angle pdb=" CA PHE A 542 " pdb=" C PHE A 542 " pdb=" N PRO A 543 " ideal model delta sigma weight residual 118.44 126.47 -8.03 1.59e+00 3.96e-01 2.55e+01 angle pdb=" CA PHE A 542 " pdb=" C PHE A 542 " pdb=" O PHE A 542 " ideal model delta sigma weight residual 120.16 114.14 6.02 1.37e+00 5.33e-01 1.93e+01 angle pdb=" N PRO A 543 " pdb=" CA PRO A 543 " pdb=" C PRO A 543 " ideal model delta sigma weight residual 114.27 109.53 4.74 1.35e+00 5.49e-01 1.23e+01 angle pdb=" C PHE A 542 " pdb=" N PRO A 543 " pdb=" CA PRO A 543 " ideal model delta sigma weight residual 120.04 116.43 3.61 1.08e+00 8.57e-01 1.12e+01 angle pdb=" N VAL B 827 " pdb=" CA VAL B 827 " pdb=" C VAL B 827 " ideal model delta sigma weight residual 112.29 109.19 3.10 9.40e-01 1.13e+00 1.08e+01 ... (remaining 8899 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.40: 3743 16.40 - 32.79: 111 32.79 - 49.19: 20 49.19 - 65.58: 1 65.58 - 81.98: 3 Dihedral angle restraints: 3878 sinusoidal: 1540 harmonic: 2338 Sorted by residual: dihedral pdb=" CA SER A 539 " pdb=" C SER A 539 " pdb=" N THR A 540 " pdb=" CA THR A 540 " ideal model delta harmonic sigma weight residual 180.00 161.25 18.75 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CB GLU B 952 " pdb=" CG GLU B 952 " pdb=" CD GLU B 952 " pdb=" OE1 GLU B 952 " ideal model delta sinusoidal sigma weight residual 0.00 -81.98 81.98 1 3.00e+01 1.11e-03 9.18e+00 dihedral pdb=" N TYR A 635 " pdb=" CA TYR A 635 " pdb=" CB TYR A 635 " pdb=" CG TYR A 635 " ideal model delta sinusoidal sigma weight residual -60.00 -110.96 50.96 3 1.50e+01 4.44e-03 8.96e+00 ... (remaining 3875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 561 0.027 - 0.053: 264 0.053 - 0.080: 49 0.080 - 0.107: 63 0.107 - 0.133: 24 Chirality restraints: 961 Sorted by residual: chirality pdb=" CA ASN A 541 " pdb=" N ASN A 541 " pdb=" C ASN A 541 " pdb=" CB ASN A 541 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA ILE A 490 " pdb=" N ILE A 490 " pdb=" C ILE A 490 " pdb=" CB ILE A 490 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.86e-01 chirality pdb=" CB VAL A 691 " pdb=" CA VAL A 691 " pdb=" CG1 VAL A 691 " pdb=" CG2 VAL A 691 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.57e-01 ... (remaining 958 not shown) Planarity restraints: 1179 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 540 " -0.015 2.00e-02 2.50e+03 3.01e-02 9.07e+00 pdb=" C THR A 540 " 0.052 2.00e-02 2.50e+03 pdb=" O THR A 540 " -0.020 2.00e-02 2.50e+03 pdb=" N ASN A 541 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 532 " 0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO A 533 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 533 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 533 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 245 " -0.017 5.00e-02 4.00e+02 2.60e-02 1.08e+00 pdb=" N PRO A 246 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 246 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 246 " -0.015 5.00e-02 4.00e+02 ... (remaining 1176 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1763 2.80 - 3.33: 5581 3.33 - 3.85: 10111 3.85 - 4.38: 11704 4.38 - 4.90: 20083 Nonbonded interactions: 49242 Sorted by model distance: nonbonded pdb=" ND2 ASN B 848 " pdb=" OG SER B 851 " model vdw 2.279 3.120 nonbonded pdb=" OD2 ASP B 874 " pdb=" ND2 ASN B 875 " model vdw 2.297 3.120 nonbonded pdb=" OD1 ASP A 584 " pdb=" OG1 THR A 609 " model vdw 2.299 3.040 nonbonded pdb=" O PRO A 397 " pdb=" NZ LYS A 483 " model vdw 2.321 3.120 nonbonded pdb=" O ASP A 578 " pdb=" OG1 THR A 597 " model vdw 2.355 3.040 ... (remaining 49237 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue 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: 1.930 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 21.360 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:4.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4185 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 : 0.002 0.025 6543 Z= 0.126 Angle : 0.560 8.027 8904 Z= 0.352 Chirality : 0.040 0.133 961 Planarity : 0.003 0.034 1179 Dihedral : 7.770 81.978 2340 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.79 % Favored : 94.09 % Rotamer: Outliers : 1.98 % Allowed : 3.67 % Favored : 94.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.25), residues: 812 helix: -2.88 (0.47), residues: 50 sheet: -1.02 (0.34), residues: 196 loop : -2.74 (0.22), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 255 HIS 0.002 0.000 HIS B 881 PHE 0.005 0.001 PHE A 693 TYR 0.008 0.001 TYR A 276 ARG 0.001 0.000 ARG B 807 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 GLU cc_start: 0.7177 (mp0) cc_final: 0.6080 (tm-30) REVERT: A 555 ILE cc_start: 0.6198 (mt) cc_final: 0.5992 (tp) REVERT: A 620 ASP cc_start: 0.8656 (m-30) cc_final: 0.8429 (m-30) REVERT: B 809 LEU cc_start: 0.7996 (mt) cc_final: 0.7145 (mt) REVERT: B 927 ILE cc_start: 0.7961 (mm) cc_final: 0.6967 (mt) REVERT: B 1004 TYR cc_start: 0.6665 (m-80) cc_final: 0.6350 (m-80) outliers start: 14 outliers final: 5 residues processed: 135 average time/residue: 0.2374 time to fit residues: 40.4264 Evaluate side-chains 110 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 105 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 68 optimal weight: 0.0050 chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 41 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 73 optimal weight: 0.0030 overall best weight: 0.4406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 484 ASN ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 GLN ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 717 GLN A 766 GLN B 921 GLN ** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 943 GLN B 980 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5389 r_free = 0.5389 target = 0.322957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.5310 r_free = 0.5310 target = 0.309285 restraints weight = 33914.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.5333 r_free = 0.5333 target = 0.310593 restraints weight = 27365.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.5338 r_free = 0.5338 target = 0.311327 restraints weight = 21907.424| |-----------------------------------------------------------------------------| r_work (final): 0.5047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3719 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6543 Z= 0.174 Angle : 0.538 10.175 8904 Z= 0.279 Chirality : 0.044 0.166 961 Planarity : 0.004 0.043 1179 Dihedral : 3.325 29.691 869 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.27), residues: 812 helix: -2.04 (0.63), residues: 50 sheet: -0.61 (0.35), residues: 195 loop : -2.10 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1013 HIS 0.004 0.001 HIS A 700 PHE 0.014 0.001 PHE A 681 TYR 0.010 0.001 TYR B 920 ARG 0.005 0.001 ARG B 807 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 GLU cc_start: 0.7352 (mp0) cc_final: 0.6534 (tm-30) REVERT: A 555 ILE cc_start: 0.6512 (mt) cc_final: 0.6139 (tp) REVERT: A 591 LEU cc_start: 0.6881 (mp) cc_final: 0.6610 (mp) REVERT: A 620 ASP cc_start: 0.8695 (m-30) cc_final: 0.8321 (m-30) REVERT: A 647 HIS cc_start: 0.6527 (m-70) cc_final: 0.6240 (m-70) REVERT: B 809 LEU cc_start: 0.7524 (mt) cc_final: 0.7235 (mt) REVERT: B 873 LYS cc_start: 0.7905 (mtmt) cc_final: 0.7673 (tppt) REVERT: B 874 ASP cc_start: 0.7474 (p0) cc_final: 0.7134 (p0) REVERT: B 942 GLN cc_start: 0.6657 (tp40) cc_final: 0.6346 (tp-100) REVERT: B 955 ILE cc_start: 0.7618 (tt) cc_final: 0.7312 (pt) REVERT: B 976 MET cc_start: 0.5634 (mpp) cc_final: 0.5056 (mpp) REVERT: B 1004 TYR cc_start: 0.6979 (m-80) cc_final: 0.5951 (m-80) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.2182 time to fit residues: 30.5506 Evaluate side-chains 95 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 39 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 15 optimal weight: 20.0000 chunk 3 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 GLN A 649 GLN ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 768 ASN B 844 HIS B 875 ASN ** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 980 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5156 r_free = 0.5156 target = 0.280332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.230510 restraints weight = 21832.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.235720 restraints weight = 16862.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4812 r_free = 0.4812 target = 0.240123 restraints weight = 13646.514| |-----------------------------------------------------------------------------| r_work (final): 0.4799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4543 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6543 Z= 0.214 Angle : 0.554 7.289 8904 Z= 0.290 Chirality : 0.044 0.153 961 Planarity : 0.004 0.039 1179 Dihedral : 3.676 25.159 869 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.28), residues: 812 helix: -1.87 (0.71), residues: 42 sheet: -0.38 (0.37), residues: 191 loop : -1.84 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 699 HIS 0.005 0.001 HIS A 700 PHE 0.011 0.001 PHE A 606 TYR 0.019 0.001 TYR B 920 ARG 0.007 0.001 ARG B 872 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 GLN cc_start: 0.7498 (tm-30) cc_final: 0.7052 (tm-30) REVERT: A 620 ASP cc_start: 0.8737 (m-30) cc_final: 0.8371 (m-30) REVERT: B 874 ASP cc_start: 0.7461 (p0) cc_final: 0.6885 (p0) REVERT: B 884 PHE cc_start: 0.7086 (m-80) cc_final: 0.6709 (m-80) REVERT: B 955 ILE cc_start: 0.7972 (tt) cc_final: 0.7253 (pt) REVERT: B 976 MET cc_start: 0.5449 (mpp) cc_final: 0.4893 (mpp) REVERT: B 991 PHE cc_start: 0.5623 (p90) cc_final: 0.5004 (p90) REVERT: B 1004 TYR cc_start: 0.7214 (m-80) cc_final: 0.5897 (m-80) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.2477 time to fit residues: 32.8584 Evaluate side-chains 90 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 4 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 ASN ** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 980 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5144 r_free = 0.5144 target = 0.275206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.223544 restraints weight = 21250.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.229141 restraints weight = 16661.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.233285 restraints weight = 13675.334| |-----------------------------------------------------------------------------| r_work (final): 0.4740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4618 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 6543 Z= 0.215 Angle : 0.543 7.641 8904 Z= 0.283 Chirality : 0.045 0.310 961 Planarity : 0.004 0.048 1179 Dihedral : 3.880 25.691 869 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.29), residues: 812 helix: -1.89 (0.67), residues: 42 sheet: -0.25 (0.38), residues: 191 loop : -1.63 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 819 HIS 0.006 0.001 HIS A 700 PHE 0.016 0.001 PHE B 904 TYR 0.009 0.001 TYR B 920 ARG 0.007 0.001 ARG B 872 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 GLN cc_start: 0.7791 (tm-30) cc_final: 0.7264 (tm-30) REVERT: A 620 ASP cc_start: 0.8707 (m-30) cc_final: 0.8324 (m-30) REVERT: A 774 LYS cc_start: 0.7711 (tptt) cc_final: 0.7382 (tppt) REVERT: B 789 SER cc_start: 0.5806 (t) cc_final: 0.5472 (p) REVERT: B 874 ASP cc_start: 0.7374 (p0) cc_final: 0.6750 (p0) REVERT: B 884 PHE cc_start: 0.7152 (m-80) cc_final: 0.6773 (m-80) REVERT: B 908 ARG cc_start: 0.5249 (mtt180) cc_final: 0.4558 (mtt180) REVERT: B 976 MET cc_start: 0.5531 (mpp) cc_final: 0.4969 (mpp) REVERT: B 1004 TYR cc_start: 0.7265 (m-80) cc_final: 0.5868 (m-80) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.2689 time to fit residues: 35.0607 Evaluate side-chains 91 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 29 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 76 optimal weight: 0.1980 chunk 61 optimal weight: 0.9990 chunk 34 optimal weight: 0.0980 chunk 46 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 980 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5146 r_free = 0.5146 target = 0.274323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.224762 restraints weight = 21717.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.230455 restraints weight = 16891.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.234635 restraints weight = 13739.197| |-----------------------------------------------------------------------------| r_work (final): 0.4759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4589 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6543 Z= 0.181 Angle : 0.525 7.270 8904 Z= 0.272 Chirality : 0.044 0.305 961 Planarity : 0.004 0.040 1179 Dihedral : 3.810 25.900 869 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.29), residues: 812 helix: -1.88 (0.66), residues: 42 sheet: -0.13 (0.39), residues: 191 loop : -1.54 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 699 HIS 0.002 0.001 HIS A 647 PHE 0.008 0.001 PHE A 452 TYR 0.009 0.001 TYR B 920 ARG 0.009 0.001 ARG B 872 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 GLN cc_start: 0.7688 (tm-30) cc_final: 0.7224 (tm-30) REVERT: A 620 ASP cc_start: 0.8691 (m-30) cc_final: 0.8324 (m-30) REVERT: A 647 HIS cc_start: 0.7000 (m-70) cc_final: 0.6778 (m-70) REVERT: A 774 LYS cc_start: 0.7742 (tptt) cc_final: 0.7404 (tppt) REVERT: B 789 SER cc_start: 0.5937 (t) cc_final: 0.5584 (p) REVERT: B 874 ASP cc_start: 0.7479 (p0) cc_final: 0.6880 (p0) REVERT: B 877 ILE cc_start: 0.7583 (tt) cc_final: 0.7366 (tt) REVERT: B 884 PHE cc_start: 0.7101 (m-80) cc_final: 0.6726 (m-80) REVERT: B 954 MET cc_start: 0.7517 (mtp) cc_final: 0.7229 (mtp) REVERT: B 976 MET cc_start: 0.5681 (mpp) cc_final: 0.5102 (mpp) REVERT: B 1004 TYR cc_start: 0.7276 (m-80) cc_final: 0.5940 (m-80) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.2577 time to fit residues: 31.8681 Evaluate side-chains 87 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 17 optimal weight: 3.9990 chunk 61 optimal weight: 0.0000 chunk 14 optimal weight: 6.9990 chunk 44 optimal weight: 0.0030 chunk 31 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 875 ASN ** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5112 r_free = 0.5112 target = 0.272571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.212414 restraints weight = 17847.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.215693 restraints weight = 15026.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.217426 restraints weight = 13005.151| |-----------------------------------------------------------------------------| r_work (final): 0.4669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4828 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 6543 Z= 0.231 Angle : 0.581 6.814 8904 Z= 0.303 Chirality : 0.046 0.316 961 Planarity : 0.004 0.038 1179 Dihedral : 4.187 25.561 869 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.29), residues: 812 helix: -1.85 (0.68), residues: 40 sheet: -0.47 (0.39), residues: 198 loop : -1.48 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 699 HIS 0.004 0.001 HIS A 647 PHE 0.011 0.001 PHE A 631 TYR 0.011 0.001 TYR B 920 ARG 0.010 0.001 ARG B 872 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 620 ASP cc_start: 0.8733 (m-30) cc_final: 0.8338 (m-30) REVERT: A 774 LYS cc_start: 0.7765 (tptt) cc_final: 0.7289 (tppt) REVERT: B 789 SER cc_start: 0.5908 (t) cc_final: 0.5497 (p) REVERT: B 831 ASN cc_start: 0.8042 (p0) cc_final: 0.7515 (t0) REVERT: B 874 ASP cc_start: 0.7455 (p0) cc_final: 0.7146 (p0) REVERT: B 884 PHE cc_start: 0.7308 (m-80) cc_final: 0.6880 (m-80) REVERT: B 908 ARG cc_start: 0.5083 (mtt180) cc_final: 0.4560 (mtt180) REVERT: B 976 MET cc_start: 0.5426 (mpp) cc_final: 0.4864 (mpp) REVERT: B 981 ASN cc_start: 0.8216 (t0) cc_final: 0.7975 (t0) REVERT: B 1004 TYR cc_start: 0.7240 (m-80) cc_final: 0.6014 (m-80) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.2393 time to fit residues: 28.6771 Evaluate side-chains 86 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 3 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 867 HIS ** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5120 r_free = 0.5120 target = 0.272648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.211746 restraints weight = 18014.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.215383 restraints weight = 15174.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.218985 restraints weight = 13539.477| |-----------------------------------------------------------------------------| r_work (final): 0.4686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4821 moved from start: 0.4748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6543 Z= 0.220 Angle : 0.565 8.383 8904 Z= 0.293 Chirality : 0.045 0.286 961 Planarity : 0.004 0.045 1179 Dihedral : 4.198 26.851 869 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.29), residues: 812 helix: -1.52 (0.71), residues: 38 sheet: -0.51 (0.39), residues: 198 loop : -1.44 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 699 HIS 0.005 0.001 HIS A 700 PHE 0.010 0.001 PHE B 984 TYR 0.014 0.001 TYR B 803 ARG 0.009 0.001 ARG B 872 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 620 ASP cc_start: 0.8673 (m-30) cc_final: 0.8297 (m-30) REVERT: A 774 LYS cc_start: 0.7724 (tptt) cc_final: 0.7257 (tppt) REVERT: B 789 SER cc_start: 0.5868 (t) cc_final: 0.5462 (p) REVERT: B 831 ASN cc_start: 0.8093 (p0) cc_final: 0.7708 (t0) REVERT: B 872 ARG cc_start: 0.8624 (mmm160) cc_final: 0.8362 (mmm160) REVERT: B 874 ASP cc_start: 0.7442 (p0) cc_final: 0.7126 (p0) REVERT: B 884 PHE cc_start: 0.7263 (m-80) cc_final: 0.6830 (m-80) REVERT: B 976 MET cc_start: 0.5621 (mpp) cc_final: 0.5048 (mpp) REVERT: B 982 ARG cc_start: 0.6578 (mtp85) cc_final: 0.6295 (mtp85) REVERT: B 1004 TYR cc_start: 0.7299 (m-80) cc_final: 0.5983 (m-80) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.2277 time to fit residues: 27.3704 Evaluate side-chains 84 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 11 optimal weight: 0.0870 chunk 39 optimal weight: 0.8980 chunk 10 optimal weight: 0.0770 chunk 31 optimal weight: 4.9990 chunk 69 optimal weight: 0.5980 chunk 1 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 929 GLN ** 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 = 0.5129 r_free = 0.5129 target = 0.274426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.213768 restraints weight = 17776.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.217261 restraints weight = 15179.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.219402 restraints weight = 13264.451| |-----------------------------------------------------------------------------| r_work (final): 0.4703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4792 moved from start: 0.4815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6543 Z= 0.169 Angle : 0.543 8.099 8904 Z= 0.280 Chirality : 0.045 0.331 961 Planarity : 0.004 0.044 1179 Dihedral : 4.172 27.366 869 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.30), residues: 812 helix: -1.02 (0.77), residues: 39 sheet: -0.48 (0.39), residues: 198 loop : -1.38 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 983 HIS 0.003 0.001 HIS A 647 PHE 0.009 0.001 PHE A 452 TYR 0.007 0.001 TYR B 804 ARG 0.008 0.000 ARG B 872 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 620 ASP cc_start: 0.8613 (m-30) cc_final: 0.8376 (m-30) REVERT: B 789 SER cc_start: 0.5880 (t) cc_final: 0.5521 (p) REVERT: B 831 ASN cc_start: 0.8155 (p0) cc_final: 0.7769 (t0) REVERT: B 872 ARG cc_start: 0.8582 (mmm160) cc_final: 0.8290 (mmm160) REVERT: B 873 LYS cc_start: 0.8307 (mtmt) cc_final: 0.8002 (tppt) REVERT: B 874 ASP cc_start: 0.7509 (p0) cc_final: 0.7183 (p0) REVERT: B 884 PHE cc_start: 0.7229 (m-80) cc_final: 0.6792 (m-80) REVERT: B 908 ARG cc_start: 0.4984 (mtt180) cc_final: 0.4670 (mtt-85) REVERT: B 976 MET cc_start: 0.5676 (mpp) cc_final: 0.5133 (mpp) REVERT: B 982 ARG cc_start: 0.6579 (mtp85) cc_final: 0.6352 (mtp85) REVERT: B 1004 TYR cc_start: 0.7180 (m-80) cc_final: 0.5985 (m-80) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.2430 time to fit residues: 28.1972 Evaluate side-chains 84 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 53 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 29 optimal weight: 0.4980 chunk 64 optimal weight: 0.0010 chunk 61 optimal weight: 0.0570 chunk 19 optimal weight: 50.0000 chunk 80 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 ASN ** A 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5351 r_free = 0.5351 target = 0.318390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.5292 r_free = 0.5292 target = 0.305022 restraints weight = 33174.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.5278 r_free = 0.5278 target = 0.306111 restraints weight = 28736.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.5289 r_free = 0.5289 target = 0.306813 restraints weight = 22824.455| |-----------------------------------------------------------------------------| r_work (final): 0.5004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3976 moved from start: 0.5022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6543 Z= 0.168 Angle : 0.542 8.319 8904 Z= 0.280 Chirality : 0.045 0.292 961 Planarity : 0.004 0.045 1179 Dihedral : 4.096 27.111 869 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.30), residues: 812 helix: -0.92 (0.80), residues: 39 sheet: -0.39 (0.40), residues: 193 loop : -1.37 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 699 HIS 0.004 0.001 HIS A 435 PHE 0.012 0.001 PHE B1010 TYR 0.006 0.001 TYR A 464 ARG 0.007 0.000 ARG B 872 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 774 LYS cc_start: 0.7624 (tptt) cc_final: 0.7316 (tptt) REVERT: B 789 SER cc_start: 0.5997 (t) cc_final: 0.5672 (p) REVERT: B 831 ASN cc_start: 0.7976 (p0) cc_final: 0.7666 (t0) REVERT: B 872 ARG cc_start: 0.8458 (mmm160) cc_final: 0.8162 (mmm160) REVERT: B 873 LYS cc_start: 0.8340 (mtmt) cc_final: 0.8091 (tppt) REVERT: B 874 ASP cc_start: 0.7572 (p0) cc_final: 0.7076 (p0) REVERT: B 884 PHE cc_start: 0.6993 (m-80) cc_final: 0.6635 (m-80) REVERT: B 908 ARG cc_start: 0.4926 (mtt180) cc_final: 0.4574 (mtt180) REVERT: B 954 MET cc_start: 0.7416 (ttm) cc_final: 0.7202 (ttm) REVERT: B 976 MET cc_start: 0.5958 (mpp) cc_final: 0.5270 (mpp) REVERT: B 1004 TYR cc_start: 0.6985 (m-80) cc_final: 0.5916 (m-80) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.2450 time to fit residues: 27.1751 Evaluate side-chains 82 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 57 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 71 optimal weight: 0.0270 chunk 32 optimal weight: 0.0980 chunk 18 optimal weight: 30.0000 chunk 41 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.6242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 929 GLN ** 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 = 0.5342 r_free = 0.5342 target = 0.316973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.5282 r_free = 0.5282 target = 0.303356 restraints weight = 33128.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.5260 r_free = 0.5260 target = 0.304598 restraints weight = 29270.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.5274 r_free = 0.5274 target = 0.305303 restraints weight = 22311.372| |-----------------------------------------------------------------------------| r_work (final): 0.4972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4036 moved from start: 0.5258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6543 Z= 0.184 Angle : 0.558 8.194 8904 Z= 0.288 Chirality : 0.045 0.278 961 Planarity : 0.004 0.088 1179 Dihedral : 4.135 27.387 869 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.30), residues: 812 helix: -1.33 (0.75), residues: 43 sheet: -0.43 (0.40), residues: 191 loop : -1.35 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 983 HIS 0.006 0.001 HIS A 700 PHE 0.015 0.001 PHE A 479 TYR 0.007 0.001 TYR B 959 ARG 0.006 0.001 ARG B 872 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 774 LYS cc_start: 0.7576 (tptt) cc_final: 0.7234 (tptt) REVERT: B 789 SER cc_start: 0.5977 (t) cc_final: 0.5636 (p) REVERT: B 872 ARG cc_start: 0.8567 (mmm160) cc_final: 0.8295 (mmm160) REVERT: B 873 LYS cc_start: 0.8513 (mtmt) cc_final: 0.8207 (tppt) REVERT: B 874 ASP cc_start: 0.7640 (p0) cc_final: 0.7213 (p0) REVERT: B 877 ILE cc_start: 0.6935 (tt) cc_final: 0.6644 (tt) REVERT: B 884 PHE cc_start: 0.7046 (m-80) cc_final: 0.6678 (m-80) REVERT: B 908 ARG cc_start: 0.5139 (mtt180) cc_final: 0.4829 (mtt-85) REVERT: B 1004 TYR cc_start: 0.6938 (m-80) cc_final: 0.5891 (m-80) REVERT: B 1010 PHE cc_start: 0.6710 (m-80) cc_final: 0.5872 (m-10) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.2728 time to fit residues: 31.2588 Evaluate side-chains 84 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 65 optimal weight: 0.9980 chunk 8 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 22 optimal weight: 9.9990 chunk 27 optimal weight: 0.0570 chunk 44 optimal weight: 0.7980 chunk 5 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 929 GLN ** 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 = 0.5335 r_free = 0.5335 target = 0.316166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.5271 r_free = 0.5271 target = 0.302473 restraints weight = 33483.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.5258 r_free = 0.5258 target = 0.303381 restraints weight = 29447.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.5269 r_free = 0.5269 target = 0.304033 restraints weight = 23992.706| |-----------------------------------------------------------------------------| r_work (final): 0.4957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4072 moved from start: 0.5486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6543 Z= 0.191 Angle : 0.572 8.330 8904 Z= 0.293 Chirality : 0.045 0.247 961 Planarity : 0.004 0.084 1179 Dihedral : 4.208 26.848 869 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.30), residues: 812 helix: -1.32 (0.74), residues: 43 sheet: -0.48 (0.40), residues: 190 loop : -1.37 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 915 HIS 0.006 0.001 HIS A 700 PHE 0.016 0.001 PHE B 991 TYR 0.010 0.001 TYR B 959 ARG 0.008 0.001 ARG A 679 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2565.50 seconds wall clock time: 46 minutes 43.35 seconds (2803.35 seconds total)