Starting phenix.real_space_refine on Fri Dec 27 18:56:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h3u_32828/12_2024/8h3u_32828.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h3u_32828/12_2024/8h3u_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_32828/12_2024/8h3u_32828.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h3u_32828/12_2024/8h3u_32828.map" model { file = "/net/cci-nas-00/data/ceres_data/8h3u_32828/12_2024/8h3u_32828.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h3u_32828/12_2024/8h3u_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-5532/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: 4.41, per 1000 atoms: 0.69 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: 1.57 Conformation dependent library (CDL) restraints added in 932.6 milliseconds 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: 0.74 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: 2.06 Time building geometry restraints manager: 1.84 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: 1.590 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.050 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: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.020 ------------------------------------------------------------------------------- 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 : 0.753 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: 0.2333 time to fit residues: 39.6402 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 : 0.733 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4317 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 : 0.638 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 429 MET cc_start: -0.0475 (mtp) cc_final: -0.0749 (mtp) REVERT: A 529 GLU cc_start: 0.7072 (mp0) cc_final: 0.6199 (tm-30) REVERT: A 555 ILE cc_start: 0.6123 (mt) cc_final: 0.5651 (tp) REVERT: A 591 LEU cc_start: 0.6886 (mp) cc_final: 0.6525 (mp) REVERT: A 620 ASP cc_start: 0.8693 (m-30) cc_final: 0.8371 (m-30) REVERT: A 647 HIS cc_start: 0.6929 (m-70) cc_final: 0.6615 (m-70) REVERT: B 874 ASP cc_start: 0.6807 (p0) cc_final: 0.6561 (p0) REVERT: B 942 GLN cc_start: 0.6827 (tp40) cc_final: 0.6612 (tp-100) REVERT: B 955 ILE cc_start: 0.7897 (tt) cc_final: 0.7553 (pt) REVERT: B 976 MET cc_start: 0.5945 (mpp) cc_final: 0.5395 (mpp) REVERT: B 1004 TYR cc_start: 0.7229 (m-80) cc_final: 0.6379 (m-80) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.2296 time to fit residues: 31.9473 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 : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 20 optimal weight: 9.9990 chunk 73 optimal weight: 0.0000 chunk 79 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 742 ASN 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4434 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6543 Z= 0.186 Angle : 0.518 7.462 8904 Z= 0.271 Chirality : 0.043 0.152 961 Planarity : 0.004 0.038 1179 Dihedral : 3.436 25.841 869 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % 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: -2.17 (0.28), residues: 812 helix: -2.05 (0.65), residues: 48 sheet: -0.49 (0.36), residues: 196 loop : -1.86 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 699 HIS 0.005 0.001 HIS A 700 PHE 0.008 0.001 PHE A 606 TYR 0.016 0.001 TYR B 920 ARG 0.006 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 102 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 GLU cc_start: 0.6919 (mp0) cc_final: 0.5764 (tm-30) REVERT: A 555 ILE cc_start: 0.6196 (mt) cc_final: 0.5750 (tp) REVERT: A 565 GLN cc_start: 0.6750 (tm-30) cc_final: 0.6447 (tm-30) REVERT: A 591 LEU cc_start: 0.6833 (mp) cc_final: 0.6462 (mp) REVERT: A 620 ASP cc_start: 0.8676 (m-30) cc_final: 0.8363 (m-30) REVERT: B 874 ASP cc_start: 0.6913 (p0) cc_final: 0.6519 (p0) REVERT: B 877 ILE cc_start: 0.7730 (tt) cc_final: 0.7526 (tt) REVERT: B 884 PHE cc_start: 0.6870 (m-80) cc_final: 0.6602 (m-80) REVERT: B 955 ILE cc_start: 0.8067 (tt) cc_final: 0.7375 (pt) REVERT: B 976 MET cc_start: 0.5874 (mpp) cc_final: 0.5248 (mpp) REVERT: B 1004 TYR cc_start: 0.7314 (m-80) cc_final: 0.6262 (m-80) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.2347 time to fit residues: 30.6719 Evaluate side-chains 93 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 55 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 49 optimal weight: 0.0970 chunk 73 optimal weight: 0.2980 chunk 78 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 21 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4511 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6543 Z= 0.191 Angle : 0.511 6.947 8904 Z= 0.266 Chirality : 0.043 0.154 961 Planarity : 0.004 0.037 1179 Dihedral : 3.566 25.350 869 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % 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: -1.68 (0.68), residues: 42 sheet: -0.27 (0.38), residues: 192 loop : -1.64 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 819 HIS 0.005 0.001 HIS A 700 PHE 0.014 0.001 PHE B 991 TYR 0.010 0.001 TYR B 920 ARG 0.009 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 102 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 GLN cc_start: 0.6816 (tm-30) cc_final: 0.6454 (tm-30) REVERT: A 620 ASP cc_start: 0.8716 (m-30) cc_final: 0.8406 (m-30) REVERT: A 647 HIS cc_start: 0.7162 (m90) cc_final: 0.6959 (m-70) REVERT: B 789 SER cc_start: 0.5729 (t) cc_final: 0.5468 (p) REVERT: B 872 ARG cc_start: 0.8470 (mmm160) cc_final: 0.7823 (mmm160) REVERT: B 874 ASP cc_start: 0.6899 (p0) cc_final: 0.6457 (p0) REVERT: B 877 ILE cc_start: 0.7770 (tt) cc_final: 0.7521 (tt) REVERT: B 884 PHE cc_start: 0.6860 (m-80) cc_final: 0.6590 (m-80) REVERT: B 942 GLN cc_start: 0.7590 (tp40) cc_final: 0.7351 (tp-100) REVERT: B 976 MET cc_start: 0.5897 (mpp) cc_final: 0.5326 (mpp) REVERT: B 984 PHE cc_start: 0.4313 (m-80) cc_final: 0.4022 (m-80) REVERT: B 1004 TYR cc_start: 0.7294 (m-80) cc_final: 0.6271 (m-80) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.2335 time to fit residues: 30.4510 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 : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 1 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 39 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 19 optimal weight: 50.0000 chunk 26 optimal weight: 40.0000 chunk 15 optimal weight: 30.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 ASN ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4968 moved from start: 0.4814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 6543 Z= 0.401 Angle : 0.791 13.456 8904 Z= 0.415 Chirality : 0.049 0.199 961 Planarity : 0.005 0.065 1179 Dihedral : 5.290 24.823 869 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 22.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % Rotamer: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % 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: -2.10 (0.28), residues: 812 helix: -2.42 (0.62), residues: 46 sheet: -0.17 (0.42), residues: 167 loop : -1.82 (0.24), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 699 HIS 0.007 0.001 HIS A 700 PHE 0.023 0.002 PHE B1017 TYR 0.020 0.002 TYR B 959 ARG 0.017 0.001 ARG A 694 *********************** 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 102 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 528 PHE cc_start: 0.7523 (m-10) cc_final: 0.7121 (m-80) REVERT: A 620 ASP cc_start: 0.8774 (m-30) cc_final: 0.8529 (m-30) REVERT: B 789 SER cc_start: 0.5660 (t) cc_final: 0.5263 (p) REVERT: B 831 ASN cc_start: 0.8192 (p0) cc_final: 0.7494 (t0) REVERT: B 864 ILE cc_start: 0.8178 (mm) cc_final: 0.7484 (tt) REVERT: B 877 ILE cc_start: 0.7754 (tt) cc_final: 0.7453 (tt) REVERT: B 880 MET cc_start: 0.7118 (mtm) cc_final: 0.6780 (mtm) REVERT: B 884 PHE cc_start: 0.7007 (m-80) cc_final: 0.6655 (m-80) REVERT: B 954 MET cc_start: 0.7385 (mtp) cc_final: 0.7066 (ttm) REVERT: B 989 THR cc_start: 0.7697 (m) cc_final: 0.6591 (m) REVERT: B 1004 TYR cc_start: 0.6873 (m-80) cc_final: 0.5965 (m-80) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.2317 time to fit residues: 30.1358 Evaluate side-chains 89 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 45 optimal weight: 0.0470 chunk 19 optimal weight: 50.0000 chunk 78 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 44 optimal weight: 0.0070 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 ASN A 480 ASN A 541 ASN ** A 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 HIS ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4715 moved from start: 0.4780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6543 Z= 0.186 Angle : 0.574 5.885 8904 Z= 0.298 Chirality : 0.046 0.315 961 Planarity : 0.004 0.046 1179 Dihedral : 4.523 28.386 869 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % 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: -1.94 (0.29), residues: 812 helix: -1.48 (0.70), residues: 39 sheet: -0.53 (0.39), residues: 190 loop : -1.64 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 915 HIS 0.002 0.001 HIS A 700 PHE 0.013 0.001 PHE B 991 TYR 0.014 0.001 TYR A 458 ARG 0.009 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 98 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 620 ASP cc_start: 0.8788 (m-30) cc_final: 0.8464 (m-30) REVERT: B 789 SER cc_start: 0.5739 (t) cc_final: 0.5402 (p) REVERT: B 831 ASN cc_start: 0.8106 (p0) cc_final: 0.7497 (t0) REVERT: B 874 ASP cc_start: 0.7008 (p0) cc_final: 0.6797 (p0) REVERT: B 877 ILE cc_start: 0.7577 (tt) cc_final: 0.7366 (tt) REVERT: B 880 MET cc_start: 0.7090 (mtm) cc_final: 0.6780 (mtm) REVERT: B 884 PHE cc_start: 0.6914 (m-80) cc_final: 0.6589 (m-80) REVERT: B 976 MET cc_start: 0.5922 (mpp) cc_final: 0.5330 (mpp) REVERT: B 1004 TYR cc_start: 0.7319 (m-80) cc_final: 0.6409 (m-80) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.2532 time to fit residues: 31.7507 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 : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 57 optimal weight: 0.2980 chunk 44 optimal weight: 0.0370 chunk 65 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 overall best weight: 0.5660 ------------------------------------------------------------------------------- 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** ** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4716 moved from start: 0.4919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6543 Z= 0.190 Angle : 0.558 5.506 8904 Z= 0.291 Chirality : 0.045 0.283 961 Planarity : 0.004 0.057 1179 Dihedral : 4.292 28.192 869 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % 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: -1.86 (0.29), residues: 812 helix: -1.36 (0.72), residues: 40 sheet: -0.48 (0.40), residues: 186 loop : -1.58 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 699 HIS 0.004 0.000 HIS A 700 PHE 0.010 0.001 PHE A 479 TYR 0.011 0.001 TYR A 458 ARG 0.012 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 93 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 789 SER cc_start: 0.5758 (t) cc_final: 0.5397 (p) REVERT: B 831 ASN cc_start: 0.8057 (p0) cc_final: 0.7540 (t0) REVERT: B 872 ARG cc_start: 0.8424 (mmm160) cc_final: 0.7950 (mmm-85) REVERT: B 874 ASP cc_start: 0.7038 (p0) cc_final: 0.6575 (p0) REVERT: B 877 ILE cc_start: 0.7648 (tt) cc_final: 0.7442 (tt) REVERT: B 880 MET cc_start: 0.7126 (mtm) cc_final: 0.6801 (mtm) REVERT: B 884 PHE cc_start: 0.6924 (m-80) cc_final: 0.6610 (m-80) REVERT: B 976 MET cc_start: 0.6076 (mpp) cc_final: 0.5478 (mpp) REVERT: B 1004 TYR cc_start: 0.7363 (m-80) cc_final: 0.6404 (m-80) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.2387 time to fit residues: 28.4829 Evaluate side-chains 89 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 15 optimal weight: 30.0000 chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.1980 chunk 38 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 61 optimal weight: 0.0170 chunk 71 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 43 optimal weight: 0.0980 overall best weight: 0.3618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 GLN ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 742 ASN ** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4670 moved from start: 0.5025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 6543 Z= 0.163 Angle : 0.540 5.975 8904 Z= 0.281 Chirality : 0.045 0.266 961 Planarity : 0.004 0.048 1179 Dihedral : 4.082 28.313 869 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % 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: -1.78 (0.29), residues: 812 helix: -1.20 (0.75), residues: 40 sheet: -0.40 (0.40), residues: 186 loop : -1.55 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 699 HIS 0.003 0.000 HIS A 700 PHE 0.016 0.001 PHE B 991 TYR 0.009 0.001 TYR B 920 ARG 0.010 0.001 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 94 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 GLN cc_start: 0.6729 (tm130) cc_final: 0.6444 (tm-30) REVERT: B 789 SER cc_start: 0.5740 (t) cc_final: 0.5420 (p) REVERT: B 831 ASN cc_start: 0.7984 (p0) cc_final: 0.7514 (t0) REVERT: B 872 ARG cc_start: 0.8409 (mmm160) cc_final: 0.7990 (mmm-85) REVERT: B 874 ASP cc_start: 0.6944 (p0) cc_final: 0.6523 (p0) REVERT: B 880 MET cc_start: 0.7072 (mtm) cc_final: 0.6599 (mtm) REVERT: B 884 PHE cc_start: 0.6899 (m-80) cc_final: 0.6586 (m-80) REVERT: B 976 MET cc_start: 0.6131 (mpp) cc_final: 0.5542 (mpp) REVERT: B 984 PHE cc_start: 0.4854 (m-80) cc_final: 0.4530 (m-80) REVERT: B 1004 TYR cc_start: 0.7385 (m-80) cc_final: 0.6438 (m-80) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.2492 time to fit residues: 30.3246 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 : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 31 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4852 moved from start: 0.5497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 6543 Z= 0.261 Angle : 0.615 6.599 8904 Z= 0.322 Chirality : 0.046 0.253 961 Planarity : 0.004 0.045 1179 Dihedral : 4.507 27.255 869 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % 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: -1.93 (0.29), residues: 812 helix: -1.43 (0.75), residues: 41 sheet: -0.68 (0.40), residues: 190 loop : -1.57 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 699 HIS 0.006 0.001 HIS A 700 PHE 0.015 0.002 PHE B 991 TYR 0.014 0.002 TYR B 920 ARG 0.008 0.001 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 94 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 565 GLN cc_start: 0.6810 (tm-30) cc_final: 0.6442 (tm-30) REVERT: A 770 LYS cc_start: 0.7975 (mtpp) cc_final: 0.7530 (mtpp) REVERT: B 789 SER cc_start: 0.5848 (t) cc_final: 0.5427 (p) REVERT: B 831 ASN cc_start: 0.8058 (p0) cc_final: 0.7731 (t0) REVERT: B 864 ILE cc_start: 0.8214 (mm) cc_final: 0.7528 (tt) REVERT: B 872 ARG cc_start: 0.8428 (mmm160) cc_final: 0.7546 (tpt90) REVERT: B 877 ILE cc_start: 0.7669 (tt) cc_final: 0.7408 (tt) REVERT: B 880 MET cc_start: 0.7139 (mtm) cc_final: 0.6752 (mtm) REVERT: B 884 PHE cc_start: 0.6966 (m-80) cc_final: 0.6614 (m-80) REVERT: B 976 MET cc_start: 0.6009 (mpp) cc_final: 0.5363 (mpp) REVERT: B 982 ARG cc_start: 0.6784 (mtp180) cc_final: 0.6549 (mtp85) REVERT: B 1004 TYR cc_start: 0.7289 (m-80) cc_final: 0.6350 (m-80) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.2250 time to fit residues: 27.3257 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 : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 80 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 64 optimal weight: 0.3980 chunk 6 optimal weight: 0.0570 chunk 49 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 19 optimal weight: 40.0000 chunk 59 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4729 moved from start: 0.5512 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= 0.178 Angle : 0.569 6.158 8904 Z= 0.296 Chirality : 0.045 0.236 961 Planarity : 0.004 0.049 1179 Dihedral : 4.271 28.383 869 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: -1.87 (0.29), residues: 812 helix: -1.08 (0.77), residues: 40 sheet: -0.64 (0.41), residues: 187 loop : -1.56 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 699 HIS 0.004 0.001 HIS A 700 PHE 0.015 0.001 PHE B 991 TYR 0.009 0.001 TYR B 920 ARG 0.008 0.000 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 97 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 565 GLN cc_start: 0.6737 (tm-30) cc_final: 0.6383 (tm-30) REVERT: A 770 LYS cc_start: 0.7927 (mtpp) cc_final: 0.7489 (mtpp) REVERT: B 789 SER cc_start: 0.5929 (t) cc_final: 0.5523 (p) REVERT: B 804 TYR cc_start: 0.5415 (t80) cc_final: 0.5074 (t80) REVERT: B 872 ARG cc_start: 0.8368 (mmm160) cc_final: 0.7525 (tpt90) REVERT: B 874 ASP cc_start: 0.7150 (p0) cc_final: 0.6637 (p0) REVERT: B 877 ILE cc_start: 0.7403 (tt) cc_final: 0.7153 (tt) REVERT: B 880 MET cc_start: 0.7040 (mtm) cc_final: 0.6480 (mtm) REVERT: B 884 PHE cc_start: 0.6944 (m-80) cc_final: 0.6612 (m-80) REVERT: B 976 MET cc_start: 0.6105 (mpp) cc_final: 0.5524 (mpp) REVERT: B 982 ARG cc_start: 0.6640 (mtp180) cc_final: 0.6168 (mtp85) REVERT: B 1004 TYR cc_start: 0.7358 (m-80) cc_final: 0.6511 (m-80) REVERT: B 1010 PHE cc_start: 0.5697 (m-80) cc_final: 0.5490 (m-80) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.2182 time to fit residues: 27.2386 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 : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 17 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 11 optimal weight: 0.4980 chunk 56 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 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 = 0.5066 r_free = 0.5066 target = 0.262208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.203925 restraints weight = 17540.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.207192 restraints weight = 14968.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.210052 restraints weight = 13310.328| |-----------------------------------------------------------------------------| r_work (final): 0.4602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5045 moved from start: 0.6142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 6543 Z= 0.340 Angle : 0.697 7.645 8904 Z= 0.370 Chirality : 0.048 0.206 961 Planarity : 0.005 0.063 1179 Dihedral : 4.989 27.627 869 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 21.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.84 % Favored : 89.16 % 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: -2.01 (0.29), residues: 812 helix: -1.28 (0.83), residues: 35 sheet: -0.61 (0.40), residues: 190 loop : -1.70 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 707 HIS 0.010 0.001 HIS A 700 PHE 0.017 0.002 PHE B 991 TYR 0.013 0.002 TYR B 959 ARG 0.007 0.001 ARG B 872 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1840.89 seconds wall clock time: 34 minutes 20.36 seconds (2060.36 seconds total)