Starting phenix.real_space_refine on Sun Sep 13 22:14:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mis_23863/09_2026/7mis_23863_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mis_23863/09_2026/7mis_23863.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mis_23863/09_2026/7mis_23863.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mis_23863/09_2026/7mis_23863.map" model { file = "/net/cci-nas-00/data/ceres_data/7mis_23863/09_2026/7mis_23863_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mis_23863/09_2026/7mis_23863_trim.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.005 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: 9 Type Number sf(0) Gaussians Ca 1 9.91 5 P 4 5.49 5 Mg 2 5.21 5 S 46 5.16 5 Na 1 4.78 5 C 8258 2.51 5 N 2210 2.21 5 O 2517 1.98 5 H 12854 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Residue "C GLU 857": not complete - not flipped Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25893 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 12185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 12185 Classifications: {'peptide': 749} Link IDs: {'PTRANS': 31, 'TRANS': 717} Chain: "B" Number of atoms: 2047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2047 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain breaks: 2 Chain: "C" Number of atoms: 11603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 11603 Classifications: {'peptide': 734} Link IDs: {'PTRANS': 40, 'TRANS': 693} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 2, ' NA': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 4.79, per 1000 atoms: 0.18 Number of scatterers: 25893 At special positions: 0 Unit cell: (139.32, 138.24, 109.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Ca 1 19.99 S 46 16.00 P 4 15.00 Mg 2 11.99 Na 1 11.00 O 2517 8.00 N 2210 7.00 C 8258 6.00 H 12854 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.87 Conformation dependent library (CDL) restraints added in 996.3 milliseconds 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3070 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 11 sheets defined 60.5% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 135 through 158 Processing helix chain 'A' and resid 164 through 182 Processing helix chain 'A' and resid 184 through 206 Proline residue: A 197 - end of helix Processing helix chain 'A' and resid 206 through 220 removed outlier: 3.717A pdb=" N MET A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 228 removed outlier: 4.016A pdb=" N HIS A 226 " --> pdb=" O TYR A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 235 Processing helix chain 'A' and resid 236 through 246 Processing helix chain 'A' and resid 251 through 261 Processing helix chain 'A' and resid 265 through 269 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 301 through 311 removed outlier: 3.643A pdb=" N LEU A 305 " --> pdb=" O TYR A 301 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR A 306 " --> pdb=" O HIS A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 328 removed outlier: 3.940A pdb=" N LYS A 328 " --> pdb=" O HIS A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 391 removed outlier: 4.134A pdb=" N LEU A 378 " --> pdb=" O PRO A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 396 Processing helix chain 'A' and resid 412 through 419 Processing helix chain 'A' and resid 424 through 432 Processing helix chain 'A' and resid 446 through 451 Processing helix chain 'A' and resid 459 through 481 Processing helix chain 'A' and resid 509 through 514 Processing helix chain 'A' and resid 525 through 530 removed outlier: 4.091A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 554 removed outlier: 3.885A pdb=" N PHE A 553 " --> pdb=" O ILE A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 563 Processing helix chain 'A' and resid 564 through 569 Processing helix chain 'A' and resid 572 through 576 Processing helix chain 'A' and resid 587 through 592 removed outlier: 3.812A pdb=" N ARG A 592 " --> pdb=" O GLY A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 624 removed outlier: 3.817A pdb=" N TYR A 597 " --> pdb=" O LEU A 593 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ASP A 624 " --> pdb=" O LYS A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 655 removed outlier: 3.550A pdb=" N TRP A 635 " --> pdb=" O LYS A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 669 removed outlier: 3.725A pdb=" N ARG A 668 " --> pdb=" O LEU A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 682 Processing helix chain 'A' and resid 684 through 689 Processing helix chain 'A' and resid 690 through 702 removed outlier: 3.766A pdb=" N SER A 700 " --> pdb=" O MET A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 775 removed outlier: 3.586A pdb=" N GLU A 742 " --> pdb=" O LEU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 794 Processing helix chain 'A' and resid 800 through 817 Processing helix chain 'A' and resid 822 through 845 removed outlier: 4.387A pdb=" N SER A 827 " --> pdb=" O ASP A 823 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ARG A 828 " --> pdb=" O ALA A 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 20 Processing helix chain 'B' and resid 32 through 40 Processing helix chain 'B' and resid 45 through 58 removed outlier: 3.754A pdb=" N VAL B 56 " --> pdb=" O MET B 52 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP B 57 " --> pdb=" O ILE B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 77 Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.831A pdb=" N ALA B 89 " --> pdb=" O GLU B 85 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE B 90 " --> pdb=" O ILE B 86 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 113 Processing helix chain 'B' and resid 121 through 129 removed outlier: 3.997A pdb=" N ARG B 127 " --> pdb=" O ASP B 123 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU B 128 " --> pdb=" O GLU B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 143 removed outlier: 3.649A pdb=" N PHE B 142 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 251 Processing helix chain 'C' and resid 283 through 308 removed outlier: 3.598A pdb=" N THR C 287 " --> pdb=" O GLY C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 336 Processing helix chain 'C' and resid 358 through 375 Processing helix chain 'C' and resid 377 through 382 removed outlier: 3.614A pdb=" N LYS C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 398 Processing helix chain 'C' and resid 406 through 421 Processing helix chain 'C' and resid 422 through 424 No H-bonds generated for 'chain 'C' and resid 422 through 424' Processing helix chain 'C' and resid 426 through 443 removed outlier: 3.959A pdb=" N THR C 441 " --> pdb=" O THR C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 461 Processing helix chain 'C' and resid 501 through 505 removed outlier: 3.534A pdb=" N ASP C 504 " --> pdb=" O SER C 501 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU C 505 " --> pdb=" O LYS C 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 501 through 505' Processing helix chain 'C' and resid 523 through 528 Processing helix chain 'C' and resid 530 through 537 Processing helix chain 'C' and resid 553 through 561 removed outlier: 3.748A pdb=" N GLY C 557 " --> pdb=" O THR C 553 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN C 561 " --> pdb=" O GLY C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 584 removed outlier: 3.684A pdb=" N CYS C 566 " --> pdb=" O ASN C 562 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN C 578 " --> pdb=" O ARG C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 614 removed outlier: 3.572A pdb=" N ILE C 602 " --> pdb=" O ASN C 598 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA C 603 " --> pdb=" O MET C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 618 Processing helix chain 'C' and resid 631 through 642 Processing helix chain 'C' and resid 643 through 651 Processing helix chain 'C' and resid 653 through 666 removed outlier: 3.845A pdb=" N LYS C 657 " --> pdb=" O ASP C 653 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASP C 660 " --> pdb=" O ILE C 656 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N THR C 661 " --> pdb=" O LYS C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 690 Processing helix chain 'C' and resid 697 through 711 removed outlier: 3.963A pdb=" N HIS C 703 " --> pdb=" O THR C 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 724 removed outlier: 4.111A pdb=" N ARG C 718 " --> pdb=" O TRP C 714 " (cutoff:3.500A) Processing helix chain 'C' and resid 731 through 753 Proline residue: C 743 - end of helix Processing helix chain 'C' and resid 768 through 784 Processing helix chain 'C' and resid 794 through 805 Processing helix chain 'C' and resid 807 through 812 removed outlier: 3.752A pdb=" N MET C 810 " --> pdb=" O PHE C 807 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER C 811 " --> pdb=" O SER C 808 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 828 removed outlier: 3.906A pdb=" N LEU C 825 " --> pdb=" O ASN C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 855 through 857 No H-bonds generated for 'chain 'C' and resid 855 through 857' Processing helix chain 'C' and resid 910 through 929 Processing helix chain 'C' and resid 1056 through 1069 removed outlier: 4.563A pdb=" N GLY C1061 " --> pdb=" O LEU C1057 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLU C1062 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASP C1065 " --> pdb=" O GLY C1061 " (cutoff:3.500A) Processing helix chain 'C' and resid 1070 through 1072 No H-bonds generated for 'chain 'C' and resid 1070 through 1072' Processing helix chain 'C' and resid 1077 through 1084 removed outlier: 3.977A pdb=" N ALA C1081 " --> pdb=" O ASN C1077 " (cutoff:3.500A) Processing helix chain 'C' and resid 1104 through 1111 Processing helix chain 'C' and resid 1126 through 1137 Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 109 Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 124 Processing sheet with id=AA3, first strand: chain 'A' and resid 291 through 293 Processing sheet with id=AA4, first strand: chain 'A' and resid 346 through 350 removed outlier: 6.641A pdb=" N LEU A 346 " --> pdb=" O SER A 357 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N SER A 357 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LYS A 444 " --> pdb=" O PRO A 404 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 482 through 483 Processing sheet with id=AA6, first strand: chain 'B' and resid 27 through 29 Processing sheet with id=AA7, first strand: chain 'C' and resid 492 through 493 removed outlier: 4.059A pdb=" N ARG C 520 " --> pdb=" O ILE C 493 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 623 through 625 Processing sheet with id=AA9, first strand: chain 'C' and resid 669 through 670 removed outlier: 3.601A pdb=" N VAL C 681 " --> pdb=" O GLU C 670 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 760 through 765 removed outlier: 6.485A pdb=" N ILE C 834 " --> pdb=" O PHE C 890 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LEU C 892 " --> pdb=" O ILE C 834 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLU C 836 " --> pdb=" O LEU C 892 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ALA C 894 " --> pdb=" O GLU C 836 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LEU C 838 " --> pdb=" O ALA C 894 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N LYS C 896 " --> pdb=" O LEU C 838 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ARG C 887 " --> pdb=" O LEU C 877 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LEU C 877 " --> pdb=" O ARG C 887 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE C 889 " --> pdb=" O VAL C 875 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL C 875 " --> pdb=" O ILE C 889 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N THR C 891 " --> pdb=" O THR C 873 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 816 through 819 684 hydrogen bonds defined for protein. 1968 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: 7.42 Time building geometry restraints manager: 3.83 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: 12844 1.03 - 1.23: 12 1.23 - 1.42: 5523 1.42 - 1.61: 7697 1.61 - 1.81: 82 Bond restraints: 26158 Sorted by residual: bond pdb=" C4 AMP C2000 " pdb=" C5 AMP C2000 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" C5 AMP C2000 " pdb=" C6 AMP C2000 " ideal model delta sigma weight residual 1.490 1.404 0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" O5' ATP A1001 " pdb=" PA ATP A1001 " ideal model delta sigma weight residual 1.579 1.611 -0.032 1.10e-02 8.26e+03 8.34e+00 bond pdb=" C8 AMP C2000 " pdb=" N7 AMP C2000 " ideal model delta sigma weight residual 1.350 1.309 0.041 2.00e-02 2.50e+03 4.28e+00 bond pdb=" C5 AMP C2000 " pdb=" N7 AMP C2000 " ideal model delta sigma weight residual 1.350 1.389 -0.039 2.00e-02 2.50e+03 3.74e+00 ... (remaining 26153 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 47237 2.56 - 5.12: 89 5.12 - 7.68: 5 7.68 - 10.23: 2 10.23 - 12.79: 1 Bond angle restraints: 47334 Sorted by residual: angle pdb=" PB ATP A1001 " pdb=" O3B ATP A1001 " pdb=" PG ATP A1001 " ideal model delta sigma weight residual 139.87 132.44 7.43 1.00e+00 1.00e+00 5.52e+01 angle pdb=" PA ATP A1001 " pdb=" O3A ATP A1001 " pdb=" PB ATP A1001 " ideal model delta sigma weight residual 136.83 131.87 4.96 1.00e+00 1.00e+00 2.46e+01 angle pdb=" O1P AMP C2000 " pdb=" P AMP C2000 " pdb=" O3P AMP C2000 " ideal model delta sigma weight residual 119.90 107.11 12.79 3.00e+00 1.11e-01 1.82e+01 angle pdb=" N1 AMP C2000 " pdb=" C2 AMP C2000 " pdb=" N3 AMP C2000 " ideal model delta sigma weight residual 120.00 128.76 -8.76 3.00e+00 1.11e-01 8.53e+00 angle pdb=" C2 AMP C2000 " pdb=" N3 AMP C2000 " pdb=" C4 AMP C2000 " ideal model delta sigma weight residual 120.00 111.24 8.76 3.00e+00 1.11e-01 8.52e+00 ... (remaining 47329 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.33: 11840 28.33 - 56.66: 430 56.66 - 84.99: 44 84.99 - 113.32: 4 113.32 - 141.65: 1 Dihedral angle restraints: 12319 sinusoidal: 6755 harmonic: 5564 Sorted by residual: dihedral pdb=" C5' AMP C2000 " pdb=" O5' AMP C2000 " pdb=" P AMP C2000 " pdb=" O3P AMP C2000 " ideal model delta sinusoidal sigma weight residual -60.00 -169.31 109.31 1 2.00e+01 2.50e-03 3.19e+01 dihedral pdb=" CA LEU C 544 " pdb=" C LEU C 544 " pdb=" N GLU C 545 " pdb=" CA GLU C 545 " ideal model delta harmonic sigma weight residual -180.00 -158.01 -21.99 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CB GLU C 857 " pdb=" CG GLU C 857 " pdb=" CD GLU C 857 " pdb=" OE1 GLU C 857 " ideal model delta sinusoidal sigma weight residual 0.00 -141.65 141.65 1 3.00e+01 1.11e-03 1.90e+01 ... (remaining 12316 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1257 0.028 - 0.056: 495 0.056 - 0.085: 141 0.085 - 0.113: 67 0.113 - 0.141: 20 Chirality restraints: 1980 Sorted by residual: chirality pdb=" CA ILE A 349 " pdb=" N ILE A 349 " pdb=" C ILE A 349 " pdb=" CB ILE A 349 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" CA ILE C 901 " pdb=" N ILE C 901 " pdb=" C ILE C 901 " pdb=" CB ILE C 901 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA ILE A 134 " pdb=" N ILE A 134 " pdb=" C ILE A 134 " pdb=" CB ILE A 134 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.83e-01 ... (remaining 1977 not shown) Planarity restraints: 3859 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' AMP C2000 " -0.104 2.00e-02 2.50e+03 4.43e-02 5.39e+01 pdb=" C2 AMP C2000 " 0.014 2.00e-02 2.50e+03 pdb=" C4 AMP C2000 " 0.034 2.00e-02 2.50e+03 pdb=" C5 AMP C2000 " 0.025 2.00e-02 2.50e+03 pdb=" C6 AMP C2000 " -0.009 2.00e-02 2.50e+03 pdb=" C8 AMP C2000 " 0.032 2.00e-02 2.50e+03 pdb=" N1 AMP C2000 " -0.012 2.00e-02 2.50e+03 pdb=" N3 AMP C2000 " 0.037 2.00e-02 2.50e+03 pdb=" N6 AMP C2000 " -0.068 2.00e-02 2.50e+03 pdb=" N7 AMP C2000 " 0.031 2.00e-02 2.50e+03 pdb=" N9 AMP C2000 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 679 " -0.049 5.00e-02 4.00e+02 7.31e-02 8.54e+00 pdb=" N PRO C 680 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO C 680 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 680 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C1111 " 0.031 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO C1112 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO C1112 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C1112 " 0.027 5.00e-02 4.00e+02 ... (remaining 3856 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 863 2.16 - 2.77: 50250 2.77 - 3.38: 73169 3.38 - 3.99: 93107 3.99 - 4.60: 146618 Nonbonded interactions: 364007 Sorted by model distance: nonbonded pdb=" OD1 ASP C 697 " pdb=" H VAL C 698 " model vdw 1.552 2.450 nonbonded pdb="HE21 GLN B 50 " pdb=" OD1 ASN B 54 " model vdw 1.559 2.450 nonbonded pdb=" O TYR C 372 " pdb="HD22 ASN C 376 " model vdw 1.606 2.450 nonbonded pdb=" OE1 GLU A 735 " pdb=" H GLU A 735 " model vdw 1.614 2.450 nonbonded pdb="HE22 GLN C 609 " pdb=" OD1 ASN C 652 " model vdw 1.615 2.450 ... (remaining 364002 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: 6.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.190 Extract box with map and model: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 28.260 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 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 : 0.003 0.108 13305 Z= 0.148 Angle : 0.504 12.793 17978 Z= 0.267 Chirality : 0.037 0.141 1980 Planarity : 0.004 0.073 2325 Dihedral : 14.706 141.649 5058 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.21), residues: 1596 helix: 1.64 (0.18), residues: 850 sheet: 0.67 (0.53), residues: 99 loop : -0.82 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 500 TYR 0.020 0.001 TYR B 139 PHE 0.020 0.001 PHE C 716 TRP 0.007 0.001 TRP A 277 HIS 0.005 0.001 HIS C 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (13304) covalent geometry : angle 0.50350 / 0.27 (17978) hydrogen bonds : bond 0.12807 / 9.43 ( 684) hydrogen bonds : angle 5.24298 / 3.74 ( 1968) Misc. bond : bond 0.03615 / 1.90 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.750 Fit side-chains REVERT: A 425 PHE cc_start: 0.8416 (t80) cc_final: 0.8140 (t80) REVERT: A 821 PRO cc_start: 0.7896 (Cg_endo) cc_final: 0.7529 (Cg_exo) REVERT: B 49 LEU cc_start: 0.6942 (tp) cc_final: 0.6491 (tm) REVERT: B 52 MET cc_start: 0.6964 (mtm) cc_final: 0.6276 (ptm) REVERT: B 75 ARG cc_start: 0.6776 (tmm160) cc_final: 0.6553 (ttp-110) REVERT: B 84 GLU cc_start: 0.7142 (pm20) cc_final: 0.6848 (pm20) REVERT: B 138 ASN cc_start: 0.5977 (m110) cc_final: 0.5695 (t0) REVERT: C 291 MET cc_start: 0.8919 (mtp) cc_final: 0.8607 (mtp) REVERT: C 741 MET cc_start: 0.8369 (mmt) cc_final: 0.8121 (mmt) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 1.3808 time to fit residues: 243.2320 Evaluate side-chains 111 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 208 HIS C 469 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.136674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.098125 restraints weight = 54238.027| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.10 r_work: 0.3058 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13305 Z= 0.162 Angle : 0.524 6.472 17978 Z= 0.280 Chirality : 0.039 0.137 1980 Planarity : 0.004 0.048 2325 Dihedral : 6.084 83.060 1784 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.70 % Allowed : 6.31 % Favored : 92.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.21), residues: 1596 helix: 1.35 (0.18), residues: 879 sheet: 0.56 (0.52), residues: 99 loop : -0.88 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 690 TYR 0.010 0.001 TYR C 256 PHE 0.024 0.001 PHE C 716 TRP 0.012 0.001 TRP A 845 HIS 0.008 0.001 HIS C 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (13304) covalent geometry : angle 0.52433 / 0.28 (17978) hydrogen bonds : bond 0.05554 / 3.77 ( 684) hydrogen bonds : angle 4.51813 / 3.23 ( 1968) Misc. bond : bond 0.00031 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.725 Fit side-chains REVERT: A 425 PHE cc_start: 0.8525 (t80) cc_final: 0.8291 (t80) REVERT: A 427 ARG cc_start: 0.7430 (ttt-90) cc_final: 0.7218 (ttt-90) REVERT: A 821 PRO cc_start: 0.7884 (Cg_endo) cc_final: 0.7601 (Cg_exo) REVERT: B 49 LEU cc_start: 0.6879 (tp) cc_final: 0.6340 (tm) REVERT: B 52 MET cc_start: 0.7034 (mtm) cc_final: 0.6230 (ptm) REVERT: B 84 GLU cc_start: 0.7342 (pm20) cc_final: 0.7053 (pm20) REVERT: B 138 ASN cc_start: 0.5891 (m110) cc_final: 0.5574 (t0) REVERT: C 246 TYR cc_start: 0.6618 (t80) cc_final: 0.5874 (t80) REVERT: C 291 MET cc_start: 0.8946 (mtp) cc_final: 0.8642 (mtp) REVERT: C 632 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7941 (tt0) REVERT: C 1078 LYS cc_start: 0.4390 (OUTLIER) cc_final: 0.3473 (pttt) outliers start: 10 outliers final: 4 residues processed: 124 average time/residue: 1.3181 time to fit residues: 178.6269 Evaluate side-chains 116 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain C residue 632 GLU Chi-restraints excluded: chain C residue 1078 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 14 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 208 HIS C 609 GLN C 652 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.135952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.096947 restraints weight = 54261.943| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.90 r_work: 0.3059 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13305 Z= 0.181 Angle : 0.521 7.071 17978 Z= 0.278 Chirality : 0.039 0.137 1980 Planarity : 0.004 0.041 2325 Dihedral : 5.993 73.228 1784 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.56 % Allowed : 8.20 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.21), residues: 1596 helix: 1.32 (0.18), residues: 878 sheet: 0.42 (0.51), residues: 99 loop : -0.93 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 690 TYR 0.010 0.002 TYR C 256 PHE 0.024 0.002 PHE C 716 TRP 0.007 0.001 TRP A 277 HIS 0.007 0.001 HIS C 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (13304) covalent geometry : angle 0.52082 / 0.28 (17978) hydrogen bonds : bond 0.05521 / 3.74 ( 684) hydrogen bonds : angle 4.41820 / 3.16 ( 1968) Misc. bond : bond 0.00059 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.697 Fit side-chains REVERT: A 821 PRO cc_start: 0.7877 (Cg_endo) cc_final: 0.7589 (Cg_exo) REVERT: B 84 GLU cc_start: 0.7387 (pm20) cc_final: 0.6238 (tp30) REVERT: B 138 ASN cc_start: 0.5873 (m110) cc_final: 0.5629 (t0) REVERT: C 246 TYR cc_start: 0.6632 (t80) cc_final: 0.6384 (t80) REVERT: C 291 MET cc_start: 0.8942 (mtp) cc_final: 0.8679 (mtp) REVERT: C 1078 LYS cc_start: 0.4365 (OUTLIER) cc_final: 0.3444 (pttt) outliers start: 8 outliers final: 5 residues processed: 124 average time/residue: 1.3737 time to fit residues: 185.8880 Evaluate side-chains 118 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 112 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain C residue 1078 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 125 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 146 optimal weight: 0.7980 chunk 130 optimal weight: 0.0980 chunk 55 optimal weight: 1.9990 chunk 58 optimal weight: 0.3980 chunk 53 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 208 HIS C 609 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.137472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.099235 restraints weight = 53819.192| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.00 r_work: 0.3083 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13305 Z= 0.114 Angle : 0.481 6.282 17978 Z= 0.253 Chirality : 0.037 0.140 1980 Planarity : 0.004 0.046 2325 Dihedral : 5.659 66.894 1784 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.56 % Allowed : 8.97 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.21), residues: 1596 helix: 1.54 (0.18), residues: 877 sheet: 0.43 (0.51), residues: 99 loop : -0.86 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 690 TYR 0.009 0.001 TYR A 599 PHE 0.024 0.001 PHE C 716 TRP 0.006 0.001 TRP A 277 HIS 0.007 0.001 HIS C 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (13304) covalent geometry : angle 0.48072 / 0.25 (17978) hydrogen bonds : bond 0.04646 / 3.09 ( 684) hydrogen bonds : angle 4.22692 / 3.00 ( 1968) Misc. bond : bond 0.00036 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 0.540 Fit side-chains REVERT: A 205 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7442 (mppt) REVERT: B 75 ARG cc_start: 0.6785 (tmm160) cc_final: 0.6213 (ttp-170) REVERT: B 84 GLU cc_start: 0.7252 (pm20) cc_final: 0.6059 (tp30) REVERT: C 632 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7869 (tt0) REVERT: C 1078 LYS cc_start: 0.4389 (OUTLIER) cc_final: 0.3488 (pttt) outliers start: 8 outliers final: 5 residues processed: 127 average time/residue: 1.2776 time to fit residues: 177.9923 Evaluate side-chains 119 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain C residue 632 GLU Chi-restraints excluded: chain C residue 1078 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 30 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 157 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.135783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.096707 restraints weight = 54120.177| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.90 r_work: 0.3058 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13305 Z= 0.191 Angle : 0.525 6.939 17978 Z= 0.278 Chirality : 0.039 0.135 1980 Planarity : 0.004 0.049 2325 Dihedral : 5.808 68.455 1784 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.91 % Allowed : 10.37 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.21), residues: 1596 helix: 1.42 (0.18), residues: 878 sheet: 0.33 (0.51), residues: 99 loop : -0.94 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 796 TYR 0.009 0.002 TYR C 392 PHE 0.024 0.002 PHE C 716 TRP 0.007 0.001 TRP A 277 HIS 0.007 0.001 HIS C 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.19 (13304) covalent geometry : angle 0.52486 / 0.28 (17978) hydrogen bonds : bond 0.05338 / 3.58 ( 684) hydrogen bonds : angle 4.30233 / 3.07 ( 1968) Misc. bond : bond 0.00056 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.658 Fit side-chains REVERT: A 205 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7450 (mppt) REVERT: A 675 PHE cc_start: 0.8972 (OUTLIER) cc_final: 0.8368 (t80) REVERT: B 84 GLU cc_start: 0.7363 (pm20) cc_final: 0.6197 (tp30) REVERT: C 632 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7910 (tt0) REVERT: C 1078 LYS cc_start: 0.4411 (OUTLIER) cc_final: 0.3526 (pttt) outliers start: 13 outliers final: 6 residues processed: 124 average time/residue: 1.2990 time to fit residues: 176.2119 Evaluate side-chains 120 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 436 LYS Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain C residue 632 GLU Chi-restraints excluded: chain C residue 1078 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 132 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 130 optimal weight: 0.2980 chunk 21 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 98 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 23 optimal weight: 0.0570 chunk 14 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.137533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.099059 restraints weight = 53843.454| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.04 r_work: 0.3085 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13305 Z= 0.111 Angle : 0.478 5.953 17978 Z= 0.251 Chirality : 0.037 0.140 1980 Planarity : 0.004 0.049 2325 Dihedral : 5.520 63.964 1784 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.77 % Allowed : 10.72 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.21), residues: 1596 helix: 1.63 (0.18), residues: 882 sheet: 0.41 (0.51), residues: 99 loop : -0.90 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 427 TYR 0.009 0.001 TYR A 599 PHE 0.023 0.001 PHE C 716 TRP 0.006 0.001 TRP A 277 HIS 0.007 0.001 HIS C 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (13304) covalent geometry : angle 0.47843 / 0.25 (17978) hydrogen bonds : bond 0.04465 / 2.95 ( 684) hydrogen bonds : angle 4.13329 / 2.93 ( 1968) Misc. bond : bond 0.00038 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.724 Fit side-chains REVERT: A 205 LYS cc_start: 0.7634 (OUTLIER) cc_final: 0.7384 (mppt) REVERT: A 675 PHE cc_start: 0.8947 (OUTLIER) cc_final: 0.8507 (t80) REVERT: B 84 GLU cc_start: 0.7116 (pm20) cc_final: 0.6037 (tp30) REVERT: C 632 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7844 (tt0) REVERT: C 1078 LYS cc_start: 0.4404 (OUTLIER) cc_final: 0.3538 (pttt) outliers start: 11 outliers final: 6 residues processed: 127 average time/residue: 1.2961 time to fit residues: 180.4518 Evaluate side-chains 122 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 436 LYS Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain C residue 632 GLU Chi-restraints excluded: chain C residue 1078 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 26 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 447 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.134273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.097713 restraints weight = 54133.799| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.09 r_work: 0.3023 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 13305 Z= 0.296 Angle : 0.595 7.318 17978 Z= 0.319 Chirality : 0.044 0.146 1980 Planarity : 0.005 0.058 2325 Dihedral : 5.995 69.719 1784 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.89 % Favored : 95.05 % Rotamer: Outliers : 0.98 % Allowed : 11.42 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.21), residues: 1596 helix: 1.25 (0.17), residues: 877 sheet: 0.40 (0.50), residues: 104 loop : -1.14 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 796 TYR 0.014 0.002 TYR C 392 PHE 0.026 0.002 PHE C 716 TRP 0.009 0.002 TRP A 277 HIS 0.006 0.001 HIS C 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00714 / 0.30 (13304) covalent geometry : angle 0.59476 / 0.32 (17978) hydrogen bonds : bond 0.06179 / 4.18 ( 684) hydrogen bonds : angle 4.43797 / 3.18 ( 1968) Misc. bond : bond 0.00079 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.726 Fit side-chains revert: symmetry clash REVERT: A 205 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7459 (mppt) REVERT: A 675 PHE cc_start: 0.9063 (OUTLIER) cc_final: 0.8317 (t80) REVERT: B 52 MET cc_start: 0.6911 (mtp) cc_final: 0.6669 (mtp) REVERT: B 84 GLU cc_start: 0.7205 (pm20) cc_final: 0.6165 (tp30) REVERT: C 632 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7917 (tt0) outliers start: 14 outliers final: 8 residues processed: 130 average time/residue: 1.3210 time to fit residues: 188.1613 Evaluate side-chains 122 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 519 GLN Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 632 GLU Chi-restraints excluded: chain C residue 1078 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 34 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 141 optimal weight: 5.9990 chunk 2 optimal weight: 0.2980 chunk 149 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.137516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.098710 restraints weight = 53910.584| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.90 r_work: 0.3088 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13305 Z= 0.108 Angle : 0.489 5.894 17978 Z= 0.257 Chirality : 0.037 0.144 1980 Planarity : 0.004 0.051 2325 Dihedral : 5.538 64.722 1784 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.84 % Allowed : 11.91 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.21), residues: 1596 helix: 1.58 (0.18), residues: 882 sheet: 0.39 (0.51), residues: 99 loop : -0.96 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 427 TYR 0.010 0.001 TYR A 599 PHE 0.023 0.001 PHE C 716 TRP 0.009 0.001 TRP A 277 HIS 0.007 0.001 HIS C 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (13304) covalent geometry : angle 0.48872 / 0.26 (17978) hydrogen bonds : bond 0.04474 / 2.95 ( 684) hydrogen bonds : angle 4.14554 / 2.93 ( 1968) Misc. bond : bond 0.00027 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.719 Fit side-chains REVERT: A 205 LYS cc_start: 0.7653 (OUTLIER) cc_final: 0.7409 (mppt) REVERT: A 675 PHE cc_start: 0.9001 (OUTLIER) cc_final: 0.8470 (t80) REVERT: B 84 GLU cc_start: 0.7050 (pm20) cc_final: 0.6036 (tp30) REVERT: C 1078 LYS cc_start: 0.4401 (OUTLIER) cc_final: 0.3492 (pttt) outliers start: 12 outliers final: 4 residues processed: 131 average time/residue: 1.3668 time to fit residues: 197.0621 Evaluate side-chains 123 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain C residue 1078 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 136 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 90 optimal weight: 0.1980 chunk 40 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 159 optimal weight: 10.0000 chunk 115 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 144 optimal weight: 0.9980 chunk 149 optimal weight: 0.8980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.137222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.098517 restraints weight = 54176.548| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.90 r_work: 0.3083 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13305 Z= 0.124 Angle : 0.489 6.028 17978 Z= 0.257 Chirality : 0.037 0.140 1980 Planarity : 0.004 0.055 2325 Dihedral : 5.527 61.982 1784 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.49 % Allowed : 12.82 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.21), residues: 1596 helix: 1.66 (0.18), residues: 882 sheet: 0.39 (0.51), residues: 99 loop : -0.95 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 427 TYR 0.009 0.001 TYR A 599 PHE 0.023 0.001 PHE C 716 TRP 0.005 0.001 TRP A 277 HIS 0.007 0.001 HIS C 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (13304) covalent geometry : angle 0.48890 / 0.26 (17978) hydrogen bonds : bond 0.04533 / 3.00 ( 684) hydrogen bonds : angle 4.11021 / 2.91 ( 1968) Misc. bond : bond 0.00029 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 0.659 Fit side-chains REVERT: A 675 PHE cc_start: 0.9001 (OUTLIER) cc_final: 0.8466 (t80) REVERT: B 84 GLU cc_start: 0.7045 (pm20) cc_final: 0.6030 (tp30) REVERT: C 1078 LYS cc_start: 0.4385 (OUTLIER) cc_final: 0.3474 (pttt) outliers start: 7 outliers final: 4 residues processed: 122 average time/residue: 1.3765 time to fit residues: 185.2807 Evaluate side-chains 117 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 111 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain C residue 1078 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 51 optimal weight: 0.9990 chunk 141 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 158 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.136545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.097924 restraints weight = 53960.426| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.11 r_work: 0.3055 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13305 Z= 0.153 Angle : 0.508 6.352 17978 Z= 0.268 Chirality : 0.038 0.139 1980 Planarity : 0.004 0.058 2325 Dihedral : 5.619 62.546 1784 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.63 % Allowed : 12.54 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.21), residues: 1596 helix: 1.62 (0.18), residues: 881 sheet: 0.53 (0.50), residues: 104 loop : -1.00 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 427 TYR 0.009 0.001 TYR C 486 PHE 0.024 0.001 PHE C 716 TRP 0.006 0.001 TRP A 277 HIS 0.008 0.001 HIS C 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (13304) covalent geometry : angle 0.50811 / 0.27 (17978) hydrogen bonds : bond 0.04848 / 3.22 ( 684) hydrogen bonds : angle 4.16095 / 2.95 ( 1968) Misc. bond : bond 0.00045 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 116 time to evaluate : 0.658 Fit side-chains REVERT: A 675 PHE cc_start: 0.9027 (OUTLIER) cc_final: 0.8337 (t80) REVERT: B 84 GLU cc_start: 0.7081 (pm20) cc_final: 0.6088 (tp30) REVERT: C 1078 LYS cc_start: 0.4396 (OUTLIER) cc_final: 0.3493 (pttt) outliers start: 9 outliers final: 4 residues processed: 123 average time/residue: 1.3904 time to fit residues: 188.6413 Evaluate side-chains 120 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 114 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain C residue 1078 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 121 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 82 optimal weight: 0.0040 chunk 150 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 131 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.135510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.099135 restraints weight = 53781.336| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.91 r_work: 0.3052 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13305 Z= 0.198 Angle : 0.541 6.664 17978 Z= 0.287 Chirality : 0.039 0.135 1980 Planarity : 0.004 0.061 2325 Dihedral : 5.769 65.212 1784 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.63 % Allowed : 12.89 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.21), residues: 1596 helix: 1.47 (0.18), residues: 883 sheet: 0.48 (0.50), residues: 104 loop : -1.07 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 522 TYR 0.010 0.002 TYR C 392 PHE 0.025 0.002 PHE C 716 TRP 0.007 0.001 TRP A 277 HIS 0.008 0.001 HIS C 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 (13304) covalent geometry : angle 0.54144 / 0.29 (17978) hydrogen bonds : bond 0.05343 / 3.58 ( 684) hydrogen bonds : angle 4.26484 / 3.04 ( 1968) Misc. bond : bond 0.00059 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8255.57 seconds wall clock time: 140 minutes 21.68 seconds (8421.68 seconds total)