Starting phenix.real_space_refine on Mon Jun 16 06:19:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7thm_25898/06_2025/7thm_25898.cif Found real_map, /net/cci-nas-00/data/ceres_data/7thm_25898/06_2025/7thm_25898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7thm_25898/06_2025/7thm_25898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7thm_25898/06_2025/7thm_25898.map" model { file = "/net/cci-nas-00/data/ceres_data/7thm_25898/06_2025/7thm_25898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7thm_25898/06_2025/7thm_25898.cif" } resolution = 3.18 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= 0.000 sd= 0.076 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: 8 Type Number sf(0) Gaussians Mn 1 7.51 5 Zn 2 6.06 5 P 2 5.49 5 S 66 5.16 5 C 5908 2.51 5 N 1543 2.21 5 O 1693 1.98 5 H 9045 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18260 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 13640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 860, 13640 Classifications: {'peptide': 860} Link IDs: {'PTRANS': 30, 'TRANS': 829} Chain breaks: 11 Chain: "B" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1684 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain breaks: 2 Chain: "C" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 586 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain breaks: 1 Chain: "D" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1139 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain breaks: 4 Chain: "G" Number of atoms: 1199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1199 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain breaks: 4 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 12 Unusual residues: {' MN': 1, ' ZN': 2, 'POP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4485 SG CYS A 301 81.783 64.126 47.676 1.00 48.64 S ATOM 4562 SG CYS A 306 84.380 62.568 45.313 1.00 47.32 S ATOM 4626 SG CYS A 310 83.281 60.731 48.499 1.00 44.89 S ATOM 7312 SG CYS A 487 68.846 76.054 38.528 1.00 57.90 S ATOM 9765 SG CYS A 645 71.609 75.822 35.848 1.00 61.34 S ATOM 9775 SG CYS A 646 72.472 76.310 39.541 1.00 58.02 S Time building chain proxies: 8.95, per 1000 atoms: 0.49 Number of scatterers: 18260 At special positions: 0 Unit cell: (130.186, 99.554, 101.742, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 Mn 1 24.99 S 66 16.00 P 2 15.00 O 1693 8.00 N 1543 7.00 C 5908 6.00 H 9045 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.67 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " Number of angles added : 6 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2202 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 15 sheets defined 46.9% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 6 through 12 removed outlier: 3.853A pdb=" N CYS A 12 " --> pdb=" O LEU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 91 removed outlier: 3.568A pdb=" N ILE A 86 " --> pdb=" O HIS A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 139 through 149 removed outlier: 3.618A pdb=" N TYR A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 159 Processing helix chain 'A' and resid 169 through 176 removed outlier: 4.108A pdb=" N ARG A 173 " --> pdb=" O PRO A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 200 Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 234 through 242 removed outlier: 3.685A pdb=" N TYR A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 248 removed outlier: 4.193A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR A 248 " --> pdb=" O ILE A 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 242 through 248' Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.884A pdb=" N SER A 255 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N HIS A 256 " --> pdb=" O ALA A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 252 through 256' Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.691A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 377 removed outlier: 3.534A pdb=" N ASP A 377 " --> pdb=" O VAL A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 384 removed outlier: 4.376A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 448 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 480 removed outlier: 3.713A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 483 No H-bonds generated for 'chain 'A' and resid 481 through 483' Processing helix chain 'A' and resid 503 through 508 removed outlier: 4.030A pdb=" N LYS A 508 " --> pdb=" O PHE A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 517 removed outlier: 3.607A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 532 Processing helix chain 'A' and resid 561 through 581 removed outlier: 4.377A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 Processing helix chain 'A' and resid 621 through 626 removed outlier: 3.604A pdb=" N MET A 626 " --> pdb=" O CYS A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 639 removed outlier: 3.596A pdb=" N ARG A 631 " --> pdb=" O PRO A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 663 Processing helix chain 'A' and resid 686 through 710 Processing helix chain 'A' and resid 718 through 733 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 767 through 774 Processing helix chain 'A' and resid 778 through 791 removed outlier: 3.826A pdb=" N PHE A 782 " --> pdb=" O SER A 778 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 799 removed outlier: 3.761A pdb=" N CYS A 799 " --> pdb=" O GLU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 843 Processing helix chain 'A' and resid 856 through 867 Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 874 through 891 removed outlier: 3.628A pdb=" N ALA A 878 " --> pdb=" O ASN A 874 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 924 removed outlier: 4.011A pdb=" N MET A 924 " --> pdb=" O PHE A 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'B' and resid 99 through 109 removed outlier: 3.585A pdb=" N ASN B 105 " --> pdb=" O ASP B 101 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE B 106 " --> pdb=" O ALA B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 124 removed outlier: 4.054A pdb=" N LEU B 122 " --> pdb=" O ASN B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 142 removed outlier: 3.655A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'C' and resid 8 through 17 removed outlier: 3.833A pdb=" N LEU C 14 " --> pdb=" O SER C 10 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL C 16 " --> pdb=" O VAL C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 41 removed outlier: 4.326A pdb=" N ASP C 38 " --> pdb=" O GLN C 34 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE C 39 " --> pdb=" O LEU C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 58 removed outlier: 3.726A pdb=" N LYS C 51 " --> pdb=" O GLU C 47 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N VAL C 53 " --> pdb=" O PHE C 49 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 99 Processing helix chain 'D' and resid 100 through 111 removed outlier: 3.508A pdb=" N ILE D 106 " --> pdb=" O ALA D 102 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG D 111 " --> pdb=" O ILE D 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 106 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 removed outlier: 6.605A pdb=" N PHE A 56 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N SER A 68 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLU A 58 " --> pdb=" O ILE A 66 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 38 removed outlier: 3.621A pdb=" N ARG A 33 " --> pdb=" O PHE A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 74 Processing sheet with id=AA4, first strand: chain 'A' and resid 203 through 204 removed outlier: 6.814A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 342 through 343 Processing sheet with id=AA6, first strand: chain 'A' and resid 334 through 335 Processing sheet with id=AA7, first strand: chain 'A' and resid 345 through 347 Processing sheet with id=AA8, first strand: chain 'A' and resid 387 through 390 removed outlier: 3.553A pdb=" N VAL B 131 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 128 " --> pdb=" O ALA B 188 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLN B 158 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 397 through 400 removed outlier: 6.940A pdb=" N LEU A 673 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN A 541 " --> pdb=" O GLY A 559 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A 557 " --> pdb=" O ASN A 543 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 753 through 758 Processing sheet with id=AB2, first strand: chain 'A' and resid 816 through 820 Processing sheet with id=AB3, first strand: chain 'D' and resid 128 through 130 removed outlier: 3.956A pdb=" N GLN D 158 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU D 189 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE D 156 " --> pdb=" O LEU D 189 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 148 through 149 Processing sheet with id=AB5, first strand: chain 'G' and resid 32 through 33 Processing sheet with id=AB6, first strand: chain 'G' and resid 53 through 55 365 hydrogen bonds defined for protein. 1008 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: 6.23 Time building geometry restraints manager: 5.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9017 1.03 - 1.23: 30 1.23 - 1.42: 4009 1.42 - 1.62: 5295 1.62 - 1.81: 98 Bond restraints: 18449 Sorted by residual: bond pdb=" O POP A1004 " pdb=" P2 POP A1004 " ideal model delta sigma weight residual 1.661 1.610 0.051 2.00e-02 2.50e+03 6.59e+00 bond pdb=" O POP A1004 " pdb=" P1 POP A1004 " ideal model delta sigma weight residual 1.660 1.610 0.050 2.00e-02 2.50e+03 6.19e+00 bond pdb=" O1 POP A1004 " pdb=" P1 POP A1004 " ideal model delta sigma weight residual 1.531 1.509 0.022 2.00e-02 2.50e+03 1.25e+00 bond pdb=" C TYR A 831 " pdb=" N PRO A 832 " ideal model delta sigma weight residual 1.326 1.342 -0.016 1.44e-02 4.82e+03 1.22e+00 bond pdb=" O2 POP A1004 " pdb=" P1 POP A1004 " ideal model delta sigma weight residual 1.531 1.509 0.022 2.00e-02 2.50e+03 1.16e+00 ... (remaining 18444 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.78: 33182 3.78 - 7.55: 11 7.55 - 11.33: 1 11.33 - 15.10: 0 15.10 - 18.88: 1 Bond angle restraints: 33195 Sorted by residual: angle pdb=" P1 POP A1004 " pdb=" O POP A1004 " pdb=" P2 POP A1004 " ideal model delta sigma weight residual 139.66 120.78 18.88 3.00e+00 1.11e-01 3.96e+01 angle pdb=" O POP A1004 " pdb=" P1 POP A1004 " pdb=" O2 POP A1004 " ideal model delta sigma weight residual 102.11 109.86 -7.75 3.00e+00 1.11e-01 6.68e+00 angle pdb=" N ALA A 399 " pdb=" CA ALA A 399 " pdb=" C ALA A 399 " ideal model delta sigma weight residual 108.46 112.23 -3.77 1.51e+00 4.39e-01 6.23e+00 angle pdb=" O POP A1004 " pdb=" P2 POP A1004 " pdb=" O4 POP A1004 " ideal model delta sigma weight residual 102.05 108.54 -6.49 3.00e+00 1.11e-01 4.67e+00 angle pdb=" N PRO A 339 " pdb=" CA PRO A 339 " pdb=" C PRO A 339 " ideal model delta sigma weight residual 110.21 113.54 -3.33 1.64e+00 3.72e-01 4.12e+00 ... (remaining 33190 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 7924 17.11 - 34.22: 608 34.22 - 51.32: 136 51.32 - 68.43: 47 68.43 - 85.54: 7 Dihedral angle restraints: 8722 sinusoidal: 4628 harmonic: 4094 Sorted by residual: dihedral pdb=" CA ASP C 44 " pdb=" C ASP C 44 " pdb=" N THR C 45 " pdb=" CA THR C 45 " ideal model delta harmonic sigma weight residual -180.00 -158.73 -21.27 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA LYS C 43 " pdb=" C LYS C 43 " pdb=" N ASP C 44 " pdb=" CA ASP C 44 " ideal model delta harmonic sigma weight residual 180.00 159.22 20.78 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA ASN A 39 " pdb=" C ASN A 39 " pdb=" N ASP A 40 " pdb=" CA ASP A 40 " ideal model delta harmonic sigma weight residual 180.00 160.33 19.67 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 8719 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 887 0.027 - 0.054: 354 0.054 - 0.081: 103 0.081 - 0.107: 64 0.107 - 0.134: 31 Chirality restraints: 1439 Sorted by residual: chirality pdb=" CA VAL A 42 " pdb=" N VAL A 42 " pdb=" C VAL A 42 " pdb=" CB VAL A 42 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" CA ILE G 91 " pdb=" N ILE G 91 " pdb=" C ILE G 91 " pdb=" CB ILE G 91 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA ILE D 120 " pdb=" N ILE D 120 " pdb=" C ILE D 120 " pdb=" CB ILE D 120 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 1436 not shown) Planarity restraints: 2688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 726 " 0.153 9.50e-02 1.11e+02 5.12e-02 3.24e+00 pdb=" NE ARG A 726 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 726 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 726 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 726 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A 726 " -0.005 2.00e-02 2.50e+03 pdb="HH12 ARG A 726 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 726 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 726 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE D 120 " 0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO D 121 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO D 121 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 121 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 808 " -0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PRO A 809 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 809 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 809 " -0.017 5.00e-02 4.00e+02 ... (remaining 2685 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 690 2.17 - 2.77: 35198 2.77 - 3.38: 49354 3.38 - 3.99: 63149 3.99 - 4.60: 99431 Nonbonded interactions: 247822 Sorted by model distance: nonbonded pdb=" OE1 GLN A 210 " pdb=" HH TYR A 237 " model vdw 1.556 2.450 nonbonded pdb=" O GLU A 144 " pdb=" HG1 THR A 148 " model vdw 1.587 2.450 nonbonded pdb=" OD2 ASP A 291 " pdb=" H ASN G 96 " model vdw 1.592 2.450 nonbonded pdb=" HG1 THR B 148 " pdb=" O ALA B 152 " model vdw 1.612 2.450 nonbonded pdb=" OD1 ASP D 161 " pdb=" H LYS D 165 " model vdw 1.616 2.450 ... (remaining 247817 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 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: 0.320 Extract box with map and model: 0.680 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 45.410 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 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 0.051 9412 Z= 0.103 Angle : 0.499 18.876 12739 Z= 0.253 Chirality : 0.038 0.134 1439 Planarity : 0.003 0.067 1604 Dihedral : 13.360 85.539 3381 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.26), residues: 1096 helix: 0.85 (0.26), residues: 456 sheet: -1.94 (0.50), residues: 111 loop : -1.36 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 800 HIS 0.001 0.000 HIS A 810 PHE 0.010 0.001 PHE A 741 TYR 0.015 0.001 TYR A 788 ARG 0.010 0.000 ARG A 726 Details of bonding type rmsd hydrogen bonds : bond 0.18889 ( 365) hydrogen bonds : angle 7.05302 ( 1008) metal coordination : bond 0.00580 ( 8) metal coordination : angle 1.51151 ( 6) covalent geometry : bond 0.00220 ( 9404) covalent geometry : angle 0.49790 (12733) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 101 ASP cc_start: 0.7829 (p0) cc_final: 0.7602 (p0) REVERT: D 111 ARG cc_start: 0.4633 (mmm160) cc_final: 0.4131 (mmp-170) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.5011 time to fit residues: 108.5479 Evaluate side-chains 127 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.0770 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 57 optimal weight: 0.0980 chunk 45 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.2344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 ASN D 157 GLN ** G 98 ASN ** 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 = 0.3937 r_free = 0.3937 target = 0.143006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.116451 restraints weight = 39293.563| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.41 r_work: 0.3494 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9412 Z= 0.175 Angle : 0.538 5.655 12739 Z= 0.291 Chirality : 0.041 0.144 1439 Planarity : 0.004 0.052 1604 Dihedral : 4.301 24.029 1243 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 0.20 % Allowed : 5.33 % Favored : 94.48 % 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: -0.87 (0.26), residues: 1096 helix: 0.58 (0.25), residues: 476 sheet: -2.22 (0.43), residues: 129 loop : -1.21 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 53 HIS 0.003 0.001 HIS A 752 PHE 0.011 0.001 PHE A 471 TYR 0.016 0.001 TYR A 887 ARG 0.006 0.000 ARG A 726 Details of bonding type rmsd hydrogen bonds : bond 0.05169 ( 365) hydrogen bonds : angle 5.43870 ( 1008) metal coordination : bond 0.01107 ( 8) metal coordination : angle 2.27722 ( 6) covalent geometry : bond 0.00399 ( 9404) covalent geometry : angle 0.53578 (12733) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 129 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 LYS cc_start: 0.8939 (mptt) cc_final: 0.8594 (mmtp) REVERT: D 111 ARG cc_start: 0.4733 (mmm160) cc_final: 0.4138 (mmp-170) outliers start: 2 outliers final: 2 residues processed: 130 average time/residue: 0.4854 time to fit residues: 86.9747 Evaluate side-chains 121 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 119 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain C residue 58 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 99 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 96 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 24 optimal weight: 0.0970 chunk 14 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 157 GLN ** G 98 ASN ** 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 = 0.3938 r_free = 0.3938 target = 0.143147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.116793 restraints weight = 39472.744| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.41 r_work: 0.3498 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9412 Z= 0.144 Angle : 0.499 5.368 12739 Z= 0.268 Chirality : 0.040 0.144 1439 Planarity : 0.003 0.038 1604 Dihedral : 4.288 24.601 1243 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 0.39 % Allowed : 6.41 % Favored : 93.20 % 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: -0.84 (0.26), residues: 1096 helix: 0.58 (0.25), residues: 478 sheet: -2.29 (0.43), residues: 126 loop : -1.14 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 53 HIS 0.003 0.001 HIS A 99 PHE 0.016 0.001 PHE A 471 TYR 0.012 0.001 TYR A 788 ARG 0.002 0.000 ARG A 858 Details of bonding type rmsd hydrogen bonds : bond 0.04147 ( 365) hydrogen bonds : angle 5.02605 ( 1008) metal coordination : bond 0.00830 ( 8) metal coordination : angle 1.87083 ( 6) covalent geometry : bond 0.00330 ( 9404) covalent geometry : angle 0.49756 (12733) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 131 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 LYS cc_start: 0.8942 (mptt) cc_final: 0.8591 (mmtp) REVERT: D 99 ASP cc_start: 0.8117 (t70) cc_final: 0.7661 (t0) REVERT: D 111 ARG cc_start: 0.4637 (mmm160) cc_final: 0.4150 (mmp-170) outliers start: 4 outliers final: 3 residues processed: 134 average time/residue: 0.5191 time to fit residues: 94.7733 Evaluate side-chains 125 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 122 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain C residue 58 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 71 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 109 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 105 optimal weight: 0.4980 chunk 90 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 875 GLN D 157 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.140515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.114072 restraints weight = 39678.362| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.43 r_work: 0.3462 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9412 Z= 0.200 Angle : 0.542 5.508 12739 Z= 0.293 Chirality : 0.041 0.147 1439 Planarity : 0.004 0.049 1604 Dihedral : 4.469 26.625 1243 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 0.39 % Allowed : 9.17 % Favored : 90.43 % 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: -1.06 (0.25), residues: 1096 helix: 0.44 (0.25), residues: 473 sheet: -2.33 (0.44), residues: 126 loop : -1.32 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 216 HIS 0.005 0.001 HIS A 99 PHE 0.019 0.002 PHE A 471 TYR 0.014 0.002 TYR A 887 ARG 0.005 0.000 ARG B 111 Details of bonding type rmsd hydrogen bonds : bond 0.04332 ( 365) hydrogen bonds : angle 5.01742 ( 1008) metal coordination : bond 0.01165 ( 8) metal coordination : angle 2.25770 ( 6) covalent geometry : bond 0.00463 ( 9404) covalent geometry : angle 0.54032 (12733) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 132 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 LYS cc_start: 0.8953 (mptt) cc_final: 0.8610 (mmtp) REVERT: A 818 MET cc_start: 0.6827 (ptm) cc_final: 0.6497 (ptm) REVERT: B 111 ARG cc_start: 0.7926 (ttm-80) cc_final: 0.6797 (ttp-170) REVERT: C 49 PHE cc_start: 0.6471 (m-80) cc_final: 0.6019 (m-80) REVERT: D 99 ASP cc_start: 0.8172 (t70) cc_final: 0.7788 (t0) outliers start: 4 outliers final: 2 residues processed: 135 average time/residue: 0.5192 time to fit residues: 97.2005 Evaluate side-chains 126 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 124 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain C residue 58 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 2 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 61 optimal weight: 0.0770 chunk 49 optimal weight: 0.2980 chunk 103 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 157 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.144275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.118679 restraints weight = 39578.131| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.30 r_work: 0.3515 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9412 Z= 0.105 Angle : 0.474 5.146 12739 Z= 0.253 Chirality : 0.039 0.145 1439 Planarity : 0.003 0.030 1604 Dihedral : 4.236 25.783 1243 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 0.79 % Allowed : 9.37 % Favored : 89.84 % 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: -0.71 (0.26), residues: 1096 helix: 0.71 (0.25), residues: 478 sheet: -2.07 (0.45), residues: 123 loop : -1.16 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 154 HIS 0.003 0.001 HIS A 928 PHE 0.021 0.001 PHE A 471 TYR 0.011 0.001 TYR A 788 ARG 0.003 0.000 ARG B 111 Details of bonding type rmsd hydrogen bonds : bond 0.03445 ( 365) hydrogen bonds : angle 4.62732 ( 1008) metal coordination : bond 0.00641 ( 8) metal coordination : angle 1.59749 ( 6) covalent geometry : bond 0.00238 ( 9404) covalent geometry : angle 0.47303 (12733) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 LYS cc_start: 0.8910 (mptt) cc_final: 0.8555 (mmtp) REVERT: A 794 MET cc_start: 0.7882 (ttp) cc_final: 0.7633 (ttp) REVERT: A 818 MET cc_start: 0.6751 (ptm) cc_final: 0.6468 (ptm) REVERT: C 49 PHE cc_start: 0.6319 (m-80) cc_final: 0.6008 (m-80) REVERT: D 99 ASP cc_start: 0.8093 (t70) cc_final: 0.7813 (t0) outliers start: 8 outliers final: 6 residues processed: 128 average time/residue: 0.4764 time to fit residues: 85.7276 Evaluate side-chains 124 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 118 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain C residue 36 HIS Chi-restraints excluded: chain C residue 58 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 13 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 705 ASN D 157 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.140883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.115555 restraints weight = 40419.109| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.27 r_work: 0.3455 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9412 Z= 0.232 Angle : 0.554 5.401 12739 Z= 0.299 Chirality : 0.042 0.144 1439 Planarity : 0.004 0.035 1604 Dihedral : 4.484 27.407 1243 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 0.99 % Allowed : 10.06 % Favored : 88.95 % 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: -1.07 (0.26), residues: 1096 helix: 0.47 (0.25), residues: 474 sheet: -2.34 (0.44), residues: 126 loop : -1.37 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 216 HIS 0.006 0.001 HIS A 99 PHE 0.019 0.002 PHE A 471 TYR 0.014 0.002 TYR A 748 ARG 0.003 0.000 ARG A 640 Details of bonding type rmsd hydrogen bonds : bond 0.04212 ( 365) hydrogen bonds : angle 4.92656 ( 1008) metal coordination : bond 0.01372 ( 8) metal coordination : angle 2.27239 ( 6) covalent geometry : bond 0.00541 ( 9404) covalent geometry : angle 0.55179 (12733) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 LYS cc_start: 0.8976 (mptt) cc_final: 0.8631 (mmtp) REVERT: A 818 MET cc_start: 0.6812 (ptm) cc_final: 0.6539 (ptm) REVERT: C 49 PHE cc_start: 0.6331 (m-80) cc_final: 0.5890 (m-80) REVERT: D 99 ASP cc_start: 0.8249 (t70) cc_final: 0.7924 (t0) outliers start: 10 outliers final: 7 residues processed: 132 average time/residue: 0.5081 time to fit residues: 94.7306 Evaluate side-chains 131 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 124 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 155 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 80 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 157 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.142072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.116238 restraints weight = 39516.928| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.37 r_work: 0.3494 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9412 Z= 0.125 Angle : 0.486 5.159 12739 Z= 0.260 Chirality : 0.039 0.141 1439 Planarity : 0.003 0.049 1604 Dihedral : 4.310 26.929 1243 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 0.79 % Allowed : 11.05 % Favored : 88.17 % 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: -0.77 (0.26), residues: 1096 helix: 0.67 (0.25), residues: 478 sheet: -2.09 (0.46), residues: 123 loop : -1.21 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 154 HIS 0.003 0.001 HIS A 99 PHE 0.019 0.001 PHE A 471 TYR 0.011 0.001 TYR A 788 ARG 0.007 0.000 ARG B 111 Details of bonding type rmsd hydrogen bonds : bond 0.03459 ( 365) hydrogen bonds : angle 4.60385 ( 1008) metal coordination : bond 0.00791 ( 8) metal coordination : angle 1.62632 ( 6) covalent geometry : bond 0.00288 ( 9404) covalent geometry : angle 0.48511 (12733) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 LYS cc_start: 0.8970 (mptt) cc_final: 0.8605 (mmtp) REVERT: A 794 MET cc_start: 0.7829 (ttp) cc_final: 0.7588 (ttp) REVERT: A 818 MET cc_start: 0.6746 (ptm) cc_final: 0.6476 (ptm) REVERT: C 49 PHE cc_start: 0.6188 (m-80) cc_final: 0.5825 (m-80) REVERT: D 99 ASP cc_start: 0.8161 (t70) cc_final: 0.7898 (t0) outliers start: 8 outliers final: 7 residues processed: 131 average time/residue: 0.5047 time to fit residues: 91.8153 Evaluate side-chains 132 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 125 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain D residue 98 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 1 optimal weight: 6.9990 chunk 19 optimal weight: 0.1980 chunk 107 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 157 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.142939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.118186 restraints weight = 39792.078| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.22 r_work: 0.3483 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9412 Z= 0.149 Angle : 0.501 5.141 12739 Z= 0.267 Chirality : 0.040 0.140 1439 Planarity : 0.004 0.043 1604 Dihedral : 4.310 26.817 1243 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 0.99 % Allowed : 11.14 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.26), residues: 1096 helix: 0.67 (0.25), residues: 478 sheet: -2.14 (0.45), residues: 123 loop : -1.24 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 216 HIS 0.004 0.001 HIS A 99 PHE 0.020 0.001 PHE A 471 TYR 0.011 0.001 TYR A 788 ARG 0.005 0.000 ARG B 111 Details of bonding type rmsd hydrogen bonds : bond 0.03570 ( 365) hydrogen bonds : angle 4.61529 ( 1008) metal coordination : bond 0.00878 ( 8) metal coordination : angle 1.78146 ( 6) covalent geometry : bond 0.00346 ( 9404) covalent geometry : angle 0.49927 (12733) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 LYS cc_start: 0.8969 (mptt) cc_final: 0.8618 (mmtp) REVERT: A 426 LYS cc_start: 0.7965 (mptt) cc_final: 0.7717 (mptt) REVERT: A 794 MET cc_start: 0.7861 (ttp) cc_final: 0.7610 (ttp) REVERT: A 818 MET cc_start: 0.6754 (ptm) cc_final: 0.6479 (ptm) REVERT: C 49 PHE cc_start: 0.5991 (m-80) cc_final: 0.5644 (m-80) REVERT: D 99 ASP cc_start: 0.8206 (t70) cc_final: 0.7955 (t0) outliers start: 10 outliers final: 9 residues processed: 131 average time/residue: 0.4827 time to fit residues: 88.4113 Evaluate side-chains 135 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain G residue 13 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 8 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 157 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.141660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.116504 restraints weight = 40014.731| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.26 r_work: 0.3475 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9412 Z= 0.175 Angle : 0.520 5.544 12739 Z= 0.278 Chirality : 0.041 0.141 1439 Planarity : 0.004 0.041 1604 Dihedral : 4.404 27.740 1243 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 1.08 % Allowed : 11.64 % Favored : 87.28 % 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: -0.89 (0.26), residues: 1096 helix: 0.58 (0.25), residues: 480 sheet: -2.18 (0.45), residues: 123 loop : -1.29 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 216 HIS 0.004 0.001 HIS A 99 PHE 0.020 0.001 PHE A 471 TYR 0.013 0.001 TYR A 788 ARG 0.005 0.000 ARG B 111 Details of bonding type rmsd hydrogen bonds : bond 0.03734 ( 365) hydrogen bonds : angle 4.68675 ( 1008) metal coordination : bond 0.01050 ( 8) metal coordination : angle 1.92142 ( 6) covalent geometry : bond 0.00407 ( 9404) covalent geometry : angle 0.51803 (12733) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 3.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 LYS cc_start: 0.8970 (mptt) cc_final: 0.8616 (mmtp) REVERT: A 426 LYS cc_start: 0.8049 (mptt) cc_final: 0.7786 (mptt) REVERT: A 794 MET cc_start: 0.7866 (ttp) cc_final: 0.7618 (ttp) REVERT: A 818 MET cc_start: 0.6897 (ptm) cc_final: 0.6634 (ptm) REVERT: C 49 PHE cc_start: 0.6397 (m-80) cc_final: 0.6050 (m-80) REVERT: D 99 ASP cc_start: 0.8211 (t70) cc_final: 0.7940 (t0) REVERT: D 127 LYS cc_start: 0.7527 (ptmm) cc_final: 0.7316 (tmtt) REVERT: D 129 MET cc_start: 0.7518 (mmm) cc_final: 0.7034 (mmm) REVERT: D 168 GLN cc_start: 0.7002 (tm-30) cc_final: 0.5820 (pp30) outliers start: 11 outliers final: 11 residues processed: 133 average time/residue: 0.5316 time to fit residues: 100.2175 Evaluate side-chains 137 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain C residue 36 HIS Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain G residue 13 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 49 optimal weight: 2.9990 chunk 31 optimal weight: 0.4980 chunk 48 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 111 optimal weight: 0.0470 overall best weight: 0.6482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 157 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.143404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.117985 restraints weight = 39667.483| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.31 r_work: 0.3512 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9412 Z= 0.114 Angle : 0.477 5.019 12739 Z= 0.253 Chirality : 0.039 0.139 1439 Planarity : 0.003 0.039 1604 Dihedral : 4.210 26.434 1243 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 0.59 % Allowed : 12.43 % Favored : 86.98 % 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: -0.59 (0.26), residues: 1096 helix: 0.82 (0.25), residues: 478 sheet: -2.02 (0.46), residues: 123 loop : -1.10 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 154 HIS 0.003 0.001 HIS A 99 PHE 0.017 0.001 PHE A 471 TYR 0.010 0.001 TYR A 788 ARG 0.005 0.000 ARG B 111 Details of bonding type rmsd hydrogen bonds : bond 0.03173 ( 365) hydrogen bonds : angle 4.43444 ( 1008) metal coordination : bond 0.00628 ( 8) metal coordination : angle 1.40826 ( 6) covalent geometry : bond 0.00263 ( 9404) covalent geometry : angle 0.47606 (12733) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 127 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 LYS cc_start: 0.8940 (mptt) cc_final: 0.8611 (mmtp) REVERT: A 426 LYS cc_start: 0.8047 (mptt) cc_final: 0.7814 (mptt) REVERT: A 794 MET cc_start: 0.7826 (ttp) cc_final: 0.7593 (ttp) REVERT: A 818 MET cc_start: 0.6820 (ptm) cc_final: 0.6562 (ptm) REVERT: C 49 PHE cc_start: 0.6484 (m-80) cc_final: 0.6142 (m-80) REVERT: D 99 ASP cc_start: 0.8169 (t70) cc_final: 0.7922 (t0) REVERT: D 127 LYS cc_start: 0.7476 (ptmm) cc_final: 0.7270 (tmtt) REVERT: D 168 GLN cc_start: 0.6942 (tm-30) cc_final: 0.5818 (pp30) outliers start: 6 outliers final: 5 residues processed: 131 average time/residue: 0.4983 time to fit residues: 91.2944 Evaluate side-chains 128 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 123 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain C residue 36 HIS Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain D residue 98 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 24 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 40 optimal weight: 0.0570 chunk 7 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 157 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.143983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.118945 restraints weight = 39203.275| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.28 r_work: 0.3516 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9412 Z= 0.111 Angle : 0.475 5.012 12739 Z= 0.252 Chirality : 0.039 0.138 1439 Planarity : 0.003 0.039 1604 Dihedral : 4.135 25.837 1243 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 0.59 % Allowed : 12.52 % Favored : 86.88 % 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: -0.49 (0.26), residues: 1096 helix: 0.91 (0.25), residues: 475 sheet: -1.96 (0.45), residues: 126 loop : -1.05 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 154 HIS 0.003 0.001 HIS A 928 PHE 0.018 0.001 PHE A 471 TYR 0.010 0.001 TYR A 788 ARG 0.005 0.000 ARG B 111 Details of bonding type rmsd hydrogen bonds : bond 0.03130 ( 365) hydrogen bonds : angle 4.36383 ( 1008) metal coordination : bond 0.00659 ( 8) metal coordination : angle 1.52106 ( 6) covalent geometry : bond 0.00258 ( 9404) covalent geometry : angle 0.47442 (12733) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9574.13 seconds wall clock time: 164 minutes 37.50 seconds (9877.50 seconds total)