Starting phenix.real_space_refine on Thu Jul 24 17:01:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h3u_32828/07_2025/8h3u_32828.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h3u_32828/07_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_32828/07_2025/8h3u_32828.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h3u_32828/07_2025/8h3u_32828.map" model { file = "/net/cci-nas-00/data/ceres_data/8h3u_32828/07_2025/8h3u_32828.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h3u_32828/07_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-5711/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: 4.98, per 1000 atoms: 0.78 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: 2.54 Conformation dependent library (CDL) restraints added in 2.9 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: 0.91 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: 2.25 Time building geometry restraints manager: 2.89 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: 35.810 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 22.430 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.070 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:3.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.430 ------------------------------------------------------------------------------- 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 6557 Z= 0.131 Angle : 0.560 8.027 8932 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 Details of bonding type rmsd hydrogen bonds : bond 0.28584 ( 132) hydrogen bonds : angle 10.77635 ( 336) SS BOND : bond 0.00098 ( 14) SS BOND : angle 0.39926 ( 28) covalent geometry : bond 0.00196 ( 6543) covalent geometry : angle 0.56036 ( 8904) *********************** 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 : 1.159 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: 0.3511 time to fit residues: 59.5859 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 : 1.194 ------------------------------------------------------------------------------- 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: 0.9980 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: 3.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 73 optimal weight: 0.0470 overall best weight: 0.4492 ------------------------------------------------------------------------------- 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 = 0.5388 r_free = 0.5388 target = 0.322902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.5327 r_free = 0.5327 target = 0.309796 restraints weight = 33921.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.5326 r_free = 0.5326 target = 0.310669 restraints weight = 25687.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.5339 r_free = 0.5339 target = 0.311541 restraints weight = 21524.204| |-----------------------------------------------------------------------------| r_work (final): 0.5044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3669 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 6557 Z= 0.117 Angle : 0.550 10.530 8932 Z= 0.284 Chirality : 0.044 0.166 961 Planarity : 0.004 0.037 1179 Dihedral : 3.284 28.403 869 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % 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: -2.45 (0.27), residues: 812 helix: -2.03 (0.63), residues: 50 sheet: -0.62 (0.35), residues: 195 loop : -2.11 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 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 0.006 0.001 ARG B 872 Details of bonding type rmsd hydrogen bonds : bond 0.03644 ( 132) hydrogen bonds : angle 7.41755 ( 336) SS BOND : bond 0.00423 ( 14) SS BOND : angle 2.12017 ( 28) covalent geometry : bond 0.00266 ( 6543) covalent geometry : angle 0.53830 ( 8904) *********************** 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 : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 GLU cc_start: 0.7327 (mp0) cc_final: 0.6469 (tm-30) REVERT: A 555 ILE cc_start: 0.6545 (mt) cc_final: 0.6281 (tp) REVERT: A 620 ASP cc_start: 0.8641 (m-30) cc_final: 0.8261 (m-30) REVERT: A 647 HIS cc_start: 0.6548 (m-70) cc_final: 0.6250 (m-70) REVERT: B 808 LEU cc_start: 0.6400 (mt) cc_final: 0.4847 (mt) REVERT: B 809 LEU cc_start: 0.7539 (mt) cc_final: 0.5676 (mt) REVERT: B 874 ASP cc_start: 0.7483 (p0) cc_final: 0.7051 (p0) REVERT: B 942 GLN cc_start: 0.6681 (tp40) cc_final: 0.6339 (tp-100) REVERT: B 955 ILE cc_start: 0.7591 (tt) cc_final: 0.7284 (pt) REVERT: B 976 MET cc_start: 0.5683 (mpp) cc_final: 0.5137 (mpp) REVERT: B 1004 TYR cc_start: 0.6973 (m-80) cc_final: 0.5973 (m-80) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.2235 time to fit residues: 31.2897 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 : 0.705 ------------------------------------------------------------------------------- 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: 3.9990 chunk 15 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 70 optimal weight: 0.0870 chunk 28 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** A 768 ASN B 875 ASN ** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 980 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5110 r_free = 0.5110 target = 0.269789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.221321 restraints weight = 19667.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.226506 restraints weight = 15364.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4759 r_free = 0.4759 target = 0.230622 restraints weight = 12572.108| |-----------------------------------------------------------------------------| r_work (final): 0.4732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4632 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 6557 Z= 0.212 Angle : 0.680 8.652 8932 Z= 0.355 Chirality : 0.046 0.172 961 Planarity : 0.005 0.056 1179 Dihedral : 4.379 23.048 869 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 0.14 % Allowed : 3.25 % Favored : 96.61 % 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: -2.18 (0.28), residues: 812 helix: -2.05 (0.71), residues: 40 sheet: -0.43 (0.37), residues: 190 loop : -1.89 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 699 HIS 0.008 0.001 HIS A 700 PHE 0.018 0.002 PHE A 631 TYR 0.027 0.002 TYR B 920 ARG 0.007 0.001 ARG B 872 Details of bonding type rmsd hydrogen bonds : bond 0.04452 ( 132) hydrogen bonds : angle 7.73556 ( 336) SS BOND : bond 0.00808 ( 14) SS BOND : angle 1.57348 ( 28) covalent geometry : bond 0.00472 ( 6543) covalent geometry : angle 0.67522 ( 8904) *********************** 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: 1 poor density : 101 time to evaluate : 0.763 Fit side-chains revert: symmetry clash REVERT: A 565 GLN cc_start: 0.7743 (tm-30) cc_final: 0.7149 (tm-30) REVERT: A 579 VAL cc_start: 0.7138 (m) cc_final: 0.6891 (m) REVERT: A 620 ASP cc_start: 0.8747 (m-30) cc_final: 0.8406 (m-30) REVERT: A 661 LEU cc_start: 0.0884 (OUTLIER) cc_final: -0.1880 (mt) REVERT: A 695 ILE cc_start: 0.4785 (pt) cc_final: 0.3779 (pt) REVERT: A 764 ARG cc_start: 0.8414 (tpp80) cc_final: 0.7711 (tpp80) REVERT: B 877 ILE cc_start: 0.7477 (tt) cc_final: 0.7254 (tt) REVERT: B 884 PHE cc_start: 0.7043 (m-80) cc_final: 0.6686 (m-80) REVERT: B 942 GLN cc_start: 0.7206 (tp40) cc_final: 0.6996 (tp40) REVERT: B 954 MET cc_start: 0.7635 (mtp) cc_final: 0.7425 (mtp) REVERT: B 955 ILE cc_start: 0.8105 (tt) cc_final: 0.7155 (pt) REVERT: B 982 ARG cc_start: 0.6272 (mtp180) cc_final: 0.6026 (mtp180) REVERT: B 984 PHE cc_start: 0.5812 (m-80) cc_final: 0.5544 (m-80) REVERT: B 1004 TYR cc_start: 0.7188 (m-80) cc_final: 0.5961 (m-80) outliers start: 1 outliers final: 0 residues processed: 102 average time/residue: 0.2346 time to fit residues: 30.2264 Evaluate side-chains 89 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.678 ------------------------------------------------------------------------------- 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: 2.9990 chunk 65 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 62 optimal weight: 0.4980 chunk 42 optimal weight: 0.5980 chunk 1 optimal weight: 0.0980 chunk 52 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 ASN ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 844 HIS ** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 980 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5148 r_free = 0.5148 target = 0.273937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.226083 restraints weight = 21812.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.231844 restraints weight = 16722.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4815 r_free = 0.4815 target = 0.235899 restraints weight = 13507.582| |-----------------------------------------------------------------------------| r_work (final): 0.4779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4552 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6557 Z= 0.118 Angle : 0.549 5.327 8932 Z= 0.284 Chirality : 0.045 0.314 961 Planarity : 0.003 0.040 1179 Dihedral : 3.979 26.890 869 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % 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: -1.83 (0.29), residues: 812 helix: -1.52 (0.76), residues: 38 sheet: -0.31 (0.38), residues: 189 loop : -1.61 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 819 HIS 0.003 0.001 HIS A 700 PHE 0.010 0.001 PHE A 479 TYR 0.008 0.001 TYR A 276 ARG 0.008 0.001 ARG B 872 Details of bonding type rmsd hydrogen bonds : bond 0.03152 ( 132) hydrogen bonds : angle 6.81518 ( 336) SS BOND : bond 0.00482 ( 14) SS BOND : angle 1.48471 ( 28) covalent geometry : bond 0.00273 ( 6543) covalent geometry : angle 0.54402 ( 8904) *********************** 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 99 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 GLN cc_start: 0.7687 (tm-30) cc_final: 0.7179 (tm-30) REVERT: A 620 ASP cc_start: 0.8692 (m-30) cc_final: 0.8341 (m-30) REVERT: B 789 SER cc_start: 0.5818 (t) cc_final: 0.5470 (p) REVERT: B 874 ASP cc_start: 0.7475 (p0) cc_final: 0.7268 (p0) REVERT: B 884 PHE cc_start: 0.7044 (m-80) cc_final: 0.6687 (m-80) REVERT: B 954 MET cc_start: 0.7492 (mtp) cc_final: 0.7239 (mtp) REVERT: B 976 MET cc_start: 0.5807 (mpp) cc_final: 0.5126 (mpp) REVERT: B 982 ARG cc_start: 0.6138 (mtp180) cc_final: 0.5879 (mtp85) REVERT: B 984 PHE cc_start: 0.5410 (m-80) cc_final: 0.4854 (m-80) REVERT: B 1004 TYR cc_start: 0.7245 (m-80) cc_final: 0.5943 (m-80) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.2677 time to fit residues: 34.3006 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 : 0.714 ------------------------------------------------------------------------------- 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: 0.9990 chunk 48 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 63 optimal weight: 9.9990 chunk 67 optimal weight: 0.8980 chunk 21 optimal weight: 0.0570 chunk 57 optimal weight: 0.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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** B 980 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5363 r_free = 0.5363 target = 0.319066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.5301 r_free = 0.5301 target = 0.305507 restraints weight = 33429.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.5300 r_free = 0.5300 target = 0.307403 restraints weight = 28350.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.5313 r_free = 0.5313 target = 0.308007 restraints weight = 19465.393| |-----------------------------------------------------------------------------| r_work (final): 0.5004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3908 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6557 Z= 0.119 Angle : 0.544 7.286 8932 Z= 0.283 Chirality : 0.046 0.306 961 Planarity : 0.004 0.040 1179 Dihedral : 3.970 26.769 869 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % 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: -1.77 (0.29), residues: 812 helix: -1.53 (0.74), residues: 38 sheet: -0.39 (0.38), residues: 198 loop : -1.53 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 366 HIS 0.003 0.001 HIS A 700 PHE 0.030 0.001 PHE A 479 TYR 0.009 0.001 TYR B 920 ARG 0.009 0.000 ARG B 872 Details of bonding type rmsd hydrogen bonds : bond 0.03134 ( 132) hydrogen bonds : angle 6.39468 ( 336) SS BOND : bond 0.00323 ( 14) SS BOND : angle 1.23630 ( 28) covalent geometry : bond 0.00276 ( 6543) covalent geometry : angle 0.54053 ( 8904) *********************** 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 95 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 620 ASP cc_start: 0.8649 (m-30) cc_final: 0.8287 (m-30) REVERT: B 789 SER cc_start: 0.6004 (t) cc_final: 0.5670 (p) REVERT: B 804 TYR cc_start: 0.5978 (t80) cc_final: 0.5613 (t80) REVERT: B 872 ARG cc_start: 0.8481 (mmm160) cc_final: 0.8183 (mmm160) REVERT: B 877 ILE cc_start: 0.6999 (tt) cc_final: 0.6785 (tt) REVERT: B 884 PHE cc_start: 0.6891 (m-80) cc_final: 0.6553 (m-80) REVERT: B 954 MET cc_start: 0.7578 (mtp) cc_final: 0.7343 (mtp) REVERT: B 976 MET cc_start: 0.5898 (mpp) cc_final: 0.5153 (mpp) REVERT: B 984 PHE cc_start: 0.5211 (m-80) cc_final: 0.4934 (m-80) REVERT: B 1004 TYR cc_start: 0.7129 (m-80) cc_final: 0.5783 (m-80) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.2434 time to fit residues: 29.4587 Evaluate side-chains 83 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.699 ------------------------------------------------------------------------------- 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: 0.9990 chunk 61 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 875 ASN ** 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 = 0.5117 r_free = 0.5117 target = 0.272313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.222235 restraints weight = 20129.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.227346 restraints weight = 16046.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.230714 restraints weight = 13391.056| |-----------------------------------------------------------------------------| r_work (final): 0.4711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4754 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 6557 Z= 0.149 Angle : 0.579 5.482 8932 Z= 0.304 Chirality : 0.046 0.307 961 Planarity : 0.004 0.039 1179 Dihedral : 4.241 25.814 869 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 14.25 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: -1.80 (0.29), residues: 812 helix: -1.73 (0.71), residues: 40 sheet: -0.69 (0.38), residues: 207 loop : -1.42 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 699 HIS 0.006 0.001 HIS A 700 PHE 0.012 0.001 PHE A 693 TYR 0.010 0.001 TYR B 959 ARG 0.005 0.000 ARG B 872 Details of bonding type rmsd hydrogen bonds : bond 0.03384 ( 132) hydrogen bonds : angle 6.50907 ( 336) SS BOND : bond 0.00511 ( 14) SS BOND : angle 1.41193 ( 28) covalent geometry : bond 0.00342 ( 6543) covalent geometry : angle 0.57490 ( 8904) *********************** 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 : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 620 ASP cc_start: 0.8583 (m-30) cc_final: 0.8296 (m-30) REVERT: B 789 SER cc_start: 0.5928 (t) cc_final: 0.5492 (p) REVERT: B 831 ASN cc_start: 0.8009 (p0) cc_final: 0.7674 (t0) REVERT: B 874 ASP cc_start: 0.7494 (p0) cc_final: 0.6932 (p0) REVERT: B 877 ILE cc_start: 0.7509 (tt) cc_final: 0.7111 (tt) REVERT: B 884 PHE cc_start: 0.7001 (m-80) cc_final: 0.6614 (m-80) REVERT: B 976 MET cc_start: 0.5901 (mpp) cc_final: 0.5277 (mpp) REVERT: B 981 ASN cc_start: 0.8219 (t0) cc_final: 0.7996 (t0) REVERT: B 982 ARG cc_start: 0.6304 (mtp180) cc_final: 0.5994 (mtp85) REVERT: B 984 PHE cc_start: 0.5614 (m-80) cc_final: 0.5088 (m-80) REVERT: B 1004 TYR cc_start: 0.7196 (m-80) cc_final: 0.5867 (m-80) REVERT: B 1010 PHE cc_start: 0.6518 (m-80) cc_final: 0.5730 (m-80) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.2319 time to fit residues: 27.7897 Evaluate side-chains 83 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.642 ------------------------------------------------------------------------------- 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: 2.9990 chunk 11 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 80 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 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 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5111 r_free = 0.5111 target = 0.270718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.217827 restraints weight = 19759.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.223533 restraints weight = 15574.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.227287 restraints weight = 12892.303| |-----------------------------------------------------------------------------| r_work (final): 0.4700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4768 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6557 Z= 0.132 Angle : 0.565 5.915 8932 Z= 0.298 Chirality : 0.045 0.306 961 Planarity : 0.004 0.047 1179 Dihedral : 4.228 28.062 869 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % 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: -1.72 (0.30), residues: 812 helix: -1.39 (0.74), residues: 38 sheet: -0.61 (0.38), residues: 207 loop : -1.40 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 699 HIS 0.007 0.001 HIS A 700 PHE 0.017 0.001 PHE A 693 TYR 0.010 0.001 TYR B 920 ARG 0.010 0.001 ARG B 807 Details of bonding type rmsd hydrogen bonds : bond 0.03113 ( 132) hydrogen bonds : angle 6.22077 ( 336) SS BOND : bond 0.00363 ( 14) SS BOND : angle 1.25981 ( 28) covalent geometry : bond 0.00299 ( 6543) covalent geometry : angle 0.56185 ( 8904) *********************** 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 : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 620 ASP cc_start: 0.8609 (m-30) cc_final: 0.8228 (m-30) REVERT: B 789 SER cc_start: 0.5803 (t) cc_final: 0.5413 (p) REVERT: B 804 TYR cc_start: 0.6887 (t80) cc_final: 0.6665 (t80) REVERT: B 872 ARG cc_start: 0.8535 (mmm160) cc_final: 0.8329 (mmm160) REVERT: B 874 ASP cc_start: 0.7450 (p0) cc_final: 0.7242 (p0) REVERT: B 877 ILE cc_start: 0.7567 (tt) cc_final: 0.7181 (tt) REVERT: B 884 PHE cc_start: 0.7097 (m-80) cc_final: 0.6695 (m-80) REVERT: B 954 MET cc_start: 0.7366 (mtp) cc_final: 0.7154 (ttm) REVERT: B 976 MET cc_start: 0.5984 (mpp) cc_final: 0.5374 (mpp) REVERT: B 1004 TYR cc_start: 0.7201 (m-80) cc_final: 0.5985 (m-80) REVERT: B 1010 PHE cc_start: 0.6548 (m-80) cc_final: 0.5861 (m-80) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.2372 time to fit residues: 27.8436 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 : 0.658 ------------------------------------------------------------------------------- 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: 0.9980 chunk 39 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 31 optimal weight: 5.9990 chunk 69 optimal weight: 0.2980 chunk 1 optimal weight: 0.1980 chunk 23 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 7 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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** B 980 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5131 r_free = 0.5131 target = 0.272004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.221332 restraints weight = 21131.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.226902 restraints weight = 16647.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.231165 restraints weight = 13716.049| |-----------------------------------------------------------------------------| r_work (final): 0.4727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4740 moved from start: 0.5010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6557 Z= 0.115 Angle : 0.550 6.265 8932 Z= 0.291 Chirality : 0.045 0.291 961 Planarity : 0.004 0.043 1179 Dihedral : 4.232 27.589 869 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % 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: -1.65 (0.30), residues: 812 helix: -1.03 (0.81), residues: 38 sheet: -0.55 (0.39), residues: 196 loop : -1.37 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 915 HIS 0.004 0.001 HIS A 700 PHE 0.017 0.001 PHE B 984 TYR 0.008 0.001 TYR B 959 ARG 0.009 0.001 ARG B 807 Details of bonding type rmsd hydrogen bonds : bond 0.02791 ( 132) hydrogen bonds : angle 5.96255 ( 336) SS BOND : bond 0.00228 ( 14) SS BOND : angle 0.93659 ( 28) covalent geometry : bond 0.00262 ( 6543) covalent geometry : angle 0.54886 ( 8904) *********************** 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 91 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 620 ASP cc_start: 0.8563 (m-30) cc_final: 0.8286 (m-30) REVERT: A 690 LEU cc_start: 0.6095 (mp) cc_final: 0.5263 (tt) REVERT: B 789 SER cc_start: 0.5874 (t) cc_final: 0.5509 (p) REVERT: B 872 ARG cc_start: 0.8446 (mmm160) cc_final: 0.8233 (mmm160) REVERT: B 874 ASP cc_start: 0.7535 (p0) cc_final: 0.7110 (p0) REVERT: B 877 ILE cc_start: 0.7569 (tt) cc_final: 0.7207 (tt) REVERT: B 884 PHE cc_start: 0.7031 (m-80) cc_final: 0.6643 (m-80) REVERT: B 976 MET cc_start: 0.6105 (mpp) cc_final: 0.5457 (mpp) REVERT: B 981 ASN cc_start: 0.8086 (t0) cc_final: 0.7857 (t0) REVERT: B 1004 TYR cc_start: 0.7243 (m-80) cc_final: 0.6075 (m-80) REVERT: B 1010 PHE cc_start: 0.6405 (m-80) cc_final: 0.5756 (m-80) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.2352 time to fit residues: 27.3143 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 : 0.692 ------------------------------------------------------------------------------- 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: 0.8980 chunk 66 optimal weight: 0.0980 chunk 75 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 64 optimal weight: 0.1980 chunk 61 optimal weight: 0.0040 chunk 19 optimal weight: 50.0000 chunk 80 optimal weight: 0.5980 chunk 57 optimal weight: 0.0970 chunk 27 optimal weight: 0.0980 chunk 34 optimal weight: 0.6980 overall best weight: 0.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 GLN A 565 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5376 r_free = 0.5376 target = 0.320745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.5326 r_free = 0.5326 target = 0.307667 restraints weight = 33491.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.5314 r_free = 0.5314 target = 0.308740 restraints weight = 27343.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.5326 r_free = 0.5326 target = 0.309612 restraints weight = 20995.922| |-----------------------------------------------------------------------------| r_work (final): 0.5056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3854 moved from start: 0.5018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 6557 Z= 0.094 Angle : 0.514 6.143 8932 Z= 0.271 Chirality : 0.044 0.249 961 Planarity : 0.004 0.045 1179 Dihedral : 3.942 28.315 869 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % 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: -1.54 (0.30), residues: 812 helix: -1.01 (0.78), residues: 38 sheet: -0.32 (0.39), residues: 194 loop : -1.35 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 837 HIS 0.004 0.001 HIS A 435 PHE 0.012 0.001 PHE B 991 TYR 0.011 0.001 TYR B 804 ARG 0.007 0.001 ARG B 872 Details of bonding type rmsd hydrogen bonds : bond 0.02556 ( 132) hydrogen bonds : angle 5.45959 ( 336) SS BOND : bond 0.00166 ( 14) SS BOND : angle 0.71896 ( 28) covalent geometry : bond 0.00211 ( 6543) covalent geometry : angle 0.51325 ( 8904) *********************** 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 : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 GLN cc_start: 0.7959 (tm130) cc_final: 0.7538 (tm-30) REVERT: A 620 ASP cc_start: 0.8603 (m-30) cc_final: 0.8333 (m-30) REVERT: B 789 SER cc_start: 0.5844 (t) cc_final: 0.5549 (p) REVERT: B 874 ASP cc_start: 0.7412 (p0) cc_final: 0.7011 (p0) REVERT: B 884 PHE cc_start: 0.6951 (m-80) cc_final: 0.6606 (m-80) REVERT: B 954 MET cc_start: 0.7349 (mtp) cc_final: 0.7083 (mtp) REVERT: B 976 MET cc_start: 0.6380 (mpp) cc_final: 0.5725 (mpp) REVERT: B 981 ASN cc_start: 0.8006 (t0) cc_final: 0.7773 (t0) REVERT: B 1004 TYR cc_start: 0.7136 (m-80) cc_final: 0.5927 (m-80) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.2506 time to fit residues: 27.9332 Evaluate side-chains 81 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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: 0.0870 chunk 40 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 18 optimal weight: 30.0000 chunk 41 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 chunk 30 optimal weight: 9.9990 chunk 65 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 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 = 0.5138 r_free = 0.5138 target = 0.274415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.223807 restraints weight = 21229.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.229379 restraints weight = 16766.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.233763 restraints weight = 13798.923| |-----------------------------------------------------------------------------| r_work (final): 0.4739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4708 moved from start: 0.5222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6557 Z= 0.114 Angle : 0.552 6.952 8932 Z= 0.286 Chirality : 0.045 0.239 961 Planarity : 0.004 0.042 1179 Dihedral : 4.070 27.150 869 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % 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: -1.54 (0.30), residues: 812 helix: -1.21 (0.77), residues: 40 sheet: -0.43 (0.38), residues: 202 loop : -1.29 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 915 HIS 0.005 0.001 HIS A 700 PHE 0.014 0.001 PHE B 991 TYR 0.014 0.001 TYR B 959 ARG 0.006 0.001 ARG B 872 Details of bonding type rmsd hydrogen bonds : bond 0.02677 ( 132) hydrogen bonds : angle 5.56280 ( 336) SS BOND : bond 0.00256 ( 14) SS BOND : angle 0.97772 ( 28) covalent geometry : bond 0.00262 ( 6543) covalent geometry : angle 0.54983 ( 8904) ********************** 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 86 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 MET cc_start: -0.2696 (tpt) cc_final: -0.2957 (tpt) REVERT: A 565 GLN cc_start: 0.7706 (tm-30) cc_final: 0.7355 (tm-30) REVERT: A 620 ASP cc_start: 0.8594 (m-30) cc_final: 0.8368 (m-30) REVERT: A 690 LEU cc_start: 0.5984 (mp) cc_final: 0.5166 (tt) REVERT: B 789 SER cc_start: 0.5962 (t) cc_final: 0.5591 (p) REVERT: B 804 TYR cc_start: 0.5388 (t80) cc_final: 0.3763 (t80) REVERT: B 830 ARG cc_start: 0.5963 (mpt180) cc_final: 0.4651 (mmt-90) REVERT: B 874 ASP cc_start: 0.7395 (p0) cc_final: 0.7001 (p0) REVERT: B 884 PHE cc_start: 0.7023 (m-80) cc_final: 0.6661 (m-80) REVERT: B 954 MET cc_start: 0.7075 (mtp) cc_final: 0.6826 (mtp) REVERT: B 976 MET cc_start: 0.5959 (mpp) cc_final: 0.5312 (mpp) REVERT: B 981 ASN cc_start: 0.8107 (t0) cc_final: 0.7856 (t0) REVERT: B 1004 TYR cc_start: 0.7222 (m-80) cc_final: 0.6051 (m-80) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.2345 time to fit residues: 25.9608 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 : 0.686 ------------------------------------------------------------------------------- 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: 0.5980 chunk 8 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 51 optimal weight: 3.9990 chunk 33 optimal weight: 0.0370 chunk 22 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 44 optimal weight: 0.0870 chunk 5 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- 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 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 = 0.5127 r_free = 0.5127 target = 0.271873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.220590 restraints weight = 20671.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.226420 restraints weight = 16209.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.230522 restraints weight = 13306.870| |-----------------------------------------------------------------------------| r_work (final): 0.4730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4722 moved from start: 0.5498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6557 Z= 0.121 Angle : 0.557 6.457 8932 Z= 0.291 Chirality : 0.045 0.215 961 Planarity : 0.004 0.044 1179 Dihedral : 4.159 26.964 869 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % 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: -1.59 (0.30), residues: 812 helix: -1.35 (0.74), residues: 43 sheet: -0.50 (0.38), residues: 204 loop : -1.30 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 837 HIS 0.006 0.001 HIS A 700 PHE 0.011 0.001 PHE A 693 TYR 0.010 0.001 TYR B 959 ARG 0.012 0.001 ARG B 872 Details of bonding type rmsd hydrogen bonds : bond 0.02633 ( 132) hydrogen bonds : angle 5.69820 ( 336) SS BOND : bond 0.00305 ( 14) SS BOND : angle 1.03748 ( 28) covalent geometry : bond 0.00277 ( 6543) covalent geometry : angle 0.55532 ( 8904) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3162.37 seconds wall clock time: 56 minutes 31.68 seconds (3391.68 seconds total)