Starting phenix.real_space_refine on Mon Feb 19 21:21:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mis_23863/02_2024/7mis_23863_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mis_23863/02_2024/7mis_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mis_23863/02_2024/7mis_23863.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mis_23863/02_2024/7mis_23863.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mis_23863/02_2024/7mis_23863_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mis_23863/02_2024/7mis_23863_trim_updated.pdb" } resolution = 2.8 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= 0.005 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 "A PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 380": "OE1" <-> "OE2" Residue "A PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 426": "OE1" <-> "OE2" Residue "A ASP 433": "OD1" <-> "OD2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 557": "OD1" <-> "OD2" Residue "A PHE 710": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 84": "OE1" <-> "OE2" Residue "B GLU 141": "OE1" <-> "OE2" Residue "C TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 671": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 697": "OD1" <-> "OD2" Residue "C PHE 737": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 857": not complete - not flipped Residue "C GLU 1105": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/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 Classifications: {'RNA': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 10.77, per 1000 atoms: 0.42 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 - 3.50 Amino acid : False - 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: 20.59 Conformation dependent library (CDL) restraints added in 2.5 seconds 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... running ksdssp... Secondary structure from input PDB file: 74 helices and 7 sheets defined 52.4% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.26 Creating SS restraints... Processing helix chain 'A' and resid 136 through 157 Processing helix chain 'A' and resid 165 through 181 Processing helix chain 'A' and resid 185 through 205 Proline residue: A 197 - end of helix Processing helix chain 'A' and resid 207 through 219 removed outlier: 3.717A pdb=" N MET A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 227 Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 237 through 245 Processing helix chain 'A' and resid 252 through 260 Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 271 through 282 removed outlier: 4.160A pdb=" N TYR A 282 " --> pdb=" O LEU A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 312 removed outlier: 3.807A pdb=" N THR A 306 " --> pdb=" O HIS A 302 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG A 312 " --> pdb=" O ASN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 327 No H-bonds generated for 'chain 'A' and resid 325 through 327' Processing helix chain 'A' and resid 375 through 390 Processing helix chain 'A' and resid 392 through 395 No H-bonds generated for 'chain 'A' and resid 392 through 395' Processing helix chain 'A' and resid 412 through 418 Processing helix chain 'A' and resid 425 through 431 Processing helix chain 'A' and resid 448 through 450 No H-bonds generated for 'chain 'A' and resid 448 through 450' Processing helix chain 'A' and resid 460 through 480 Processing helix chain 'A' and resid 510 through 513 No H-bonds generated for 'chain 'A' and resid 510 through 513' Processing helix chain 'A' and resid 549 through 551 No H-bonds generated for 'chain 'A' and resid 549 through 551' Processing helix chain 'A' and resid 557 through 562 Processing helix chain 'A' and resid 565 through 568 No H-bonds generated for 'chain 'A' and resid 565 through 568' Processing helix chain 'A' and resid 573 through 575 No H-bonds generated for 'chain 'A' and resid 573 through 575' Processing helix chain 'A' and resid 588 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 594 through 622 Processing helix chain 'A' and resid 628 through 654 removed outlier: 3.550A pdb=" N TRP A 635 " --> pdb=" O LYS A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 668 removed outlier: 3.725A pdb=" N ARG A 668 " --> pdb=" O LEU A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 681 Processing helix chain 'A' and resid 685 through 688 Processing helix chain 'A' and resid 691 through 701 removed outlier: 3.766A pdb=" N SER A 700 " --> pdb=" O MET A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 774 Processing helix chain 'A' and resid 781 through 793 Processing helix chain 'A' and resid 801 through 816 Processing helix chain 'A' and resid 823 through 844 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 7 through 19 Processing helix chain 'B' and resid 33 through 39 Processing helix chain 'B' and resid 46 through 59 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) removed outlier: 5.032A pdb=" N ASP B 59 " --> pdb=" O GLU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 76 Processing helix chain 'B' and resid 83 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 103 through 112 Processing helix chain 'B' and resid 121 through 128 removed outlier: 4.392A pdb=" N ILE B 126 " --> pdb=" O ASP B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 142 No H-bonds generated for 'chain 'B' and resid 139 through 142' Processing helix chain 'C' and resid 238 through 250 Processing helix chain 'C' and resid 284 through 307 Processing helix chain 'C' and resid 325 through 337 removed outlier: 4.055A pdb=" N PHE C 337 " --> pdb=" O ILE C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 374 Processing helix chain 'C' and resid 378 through 381 No H-bonds generated for 'chain 'C' and resid 378 through 381' Processing helix chain 'C' and resid 386 through 397 Processing helix chain 'C' and resid 407 through 423 removed outlier: 4.838A pdb=" N ARG C 422 " --> pdb=" O VAL C 418 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N THR C 423 " --> pdb=" O ASP C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 442 removed outlier: 3.959A pdb=" N THR C 441 " --> pdb=" O THR C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 460 Processing helix chain 'C' and resid 502 through 504 No H-bonds generated for 'chain 'C' and resid 502 through 504' Processing helix chain 'C' and resid 524 through 529 Processing helix chain 'C' and resid 531 through 536 Processing helix chain 'C' and resid 554 through 560 Processing helix chain 'C' and resid 563 through 585 removed outlier: 3.818A pdb=" N GLN C 578 " --> pdb=" O ARG C 574 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY C 585 " --> pdb=" O ALA C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 613 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 617 No H-bonds generated for 'chain 'C' and resid 615 through 617' Processing helix chain 'C' and resid 632 through 641 Processing helix chain 'C' and resid 644 through 650 Processing helix chain 'C' and resid 654 through 664 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 689 Processing helix chain 'C' and resid 698 through 710 removed outlier: 3.963A pdb=" N HIS C 703 " --> pdb=" O THR C 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 723 removed outlier: 4.111A pdb=" N ARG C 718 " --> pdb=" O TRP C 714 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 752 Proline residue: C 743 - end of helix Processing helix chain 'C' and resid 769 through 785 removed outlier: 3.741A pdb=" N ASN C 785 " --> pdb=" O ALA C 781 " (cutoff:3.500A) Processing helix chain 'C' and resid 795 through 804 Processing helix chain 'C' and resid 809 through 811 No H-bonds generated for 'chain 'C' and resid 809 through 811' Processing helix chain 'C' and resid 822 through 827 Processing helix chain 'C' and resid 908 through 928 Proline residue: C 912 - end of helix Processing helix chain 'C' and resid 1056 through 1071 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) removed outlier: 4.346A pdb=" N THR C1070 " --> pdb=" O LYS C1066 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU C1071 " --> pdb=" O GLN C1067 " (cutoff:3.500A) Processing helix chain 'C' and resid 1077 through 1083 removed outlier: 3.977A pdb=" N ALA C1081 " --> pdb=" O ASN C1077 " (cutoff:3.500A) Processing helix chain 'C' and resid 1104 through 1112 Proline residue: C1112 - end of helix Processing helix chain 'C' and resid 1126 through 1136 Processing sheet with id= A, first strand: chain 'A' and resid 105 through 109 Processing sheet with id= B, first strand: chain 'A' and resid 121 through 124 Processing sheet with id= C, first strand: chain 'A' and resid 131 through 133 removed outlier: 5.997A pdb=" N ALA A 583 " --> pdb=" O LYS A 132 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 403 through 411 removed outlier: 6.725A pdb=" N VAL A 442 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLN A 407 " --> pdb=" O VAL A 440 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL A 440 " --> pdb=" O GLN A 407 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N SER A 409 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU A 438 " --> pdb=" O SER A 409 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N SER A 357 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU A 346 " --> pdb=" O SER A 357 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 623 through 625 Processing sheet with id= F, first strand: chain 'C' and resid 760 through 765 removed outlier: 6.565A pdb=" N TYR C 888 " --> pdb=" O ILE C 834 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N GLU C 836 " --> pdb=" O TYR C 888 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N PHE C 890 " --> pdb=" O GLU C 836 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LEU C 838 " --> pdb=" O PHE C 890 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU C 892 " --> pdb=" O LEU C 838 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS C 874 " --> pdb=" O THR C 891 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N VAL C 893 " --> pdb=" O PRO C 872 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N VAL C 895 " --> pdb=" O LEU C 870 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N LEU C 870 " --> pdb=" O VAL C 895 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 816 through 819 559 hydrogen bonds defined for protein. 1632 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: 8.98 Time building geometry restraints manager: 21.39 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: 99.67 - 106.54: 375 106.54 - 113.41: 31029 113.41 - 120.28: 8646 120.28 - 127.16: 7148 127.16 - 134.03: 136 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: 899 2.16 - 2.77: 50340 2.77 - 3.38: 73286 3.38 - 3.99: 93290 3.99 - 4.60: 146816 Nonbonded interactions: 364631 Sorted by model distance: nonbonded pdb=" OD1 ASP C 697 " pdb=" H VAL C 698 " model vdw 1.552 1.850 nonbonded pdb="HE21 GLN B 50 " pdb=" OD1 ASN B 54 " model vdw 1.559 1.850 nonbonded pdb=" O TYR C 372 " pdb="HD22 ASN C 376 " model vdw 1.606 1.850 nonbonded pdb=" OE1 GLU A 735 " pdb=" H GLU A 735 " model vdw 1.614 1.850 nonbonded pdb="HE22 GLN C 609 " pdb=" OD1 ASN C 652 " model vdw 1.615 1.850 ... (remaining 364626 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 3.130 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: 0.400 Extract box with map and model: 15.250 Check model and map are aligned: 0.370 Set scattering table: 0.250 Process input model: 79.540 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 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 13304 Z= 0.208 Angle : 0.503 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 (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: 0.91 (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 TRP 0.007 0.001 TRP A 277 HIS 0.005 0.001 HIS C 362 PHE 0.020 0.001 PHE C 716 TYR 0.020 0.001 TYR B 139 ARG 0.003 0.000 ARG A 500 *********************** 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 fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 2.195 Fit side-chains REVERT: A 425 PHE cc_start: 0.8416 (t80) cc_final: 0.8001 (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: 0.6552 (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: 0.8120 (mmt) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 3.0212 time to fit residues: 530.6883 Evaluate side-chains 111 residues out of total 1427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 2.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 GLN A 208 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.0683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13304 Z= 0.247 Angle : 0.491 6.158 17978 Z= 0.256 Chirality : 0.038 0.139 1980 Planarity : 0.004 0.050 2325 Dihedral : 6.197 88.997 1784 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.63 % Allowed : 6.24 % Favored : 93.13 % 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: 0.80 (0.21), residues: 1596 helix: 1.54 (0.18), residues: 850 sheet: 0.65 (0.53), residues: 99 loop : -0.84 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 845 HIS 0.008 0.001 HIS C 409 PHE 0.021 0.001 PHE C 716 TYR 0.009 0.001 TYR C 256 ARG 0.005 0.000 ARG C 690 *********************** 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 124 residues out of total 1427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 115 time to evaluate : 2.120 Fit side-chains revert: symmetry clash REVERT: A 425 PHE cc_start: 0.8440 (t80) cc_final: 0.8043 (t80) REVERT: A 821 PRO cc_start: 0.7866 (Cg_endo) cc_final: 0.7490 (Cg_exo) REVERT: B 52 MET cc_start: 0.6980 (mtm) cc_final: 0.6697 (mtp) REVERT: B 84 GLU cc_start: 0.7075 (pm20) cc_final: 0.6801 (pm20) REVERT: B 138 ASN cc_start: 0.5989 (m110) cc_final: 0.5727 (t0) REVERT: C 291 MET cc_start: 0.8872 (mtp) cc_final: 0.8569 (mtp) REVERT: C 741 MET cc_start: 0.8299 (mmt) cc_final: 0.8084 (mmt) REVERT: C 1078 LYS cc_start: 0.4389 (OUTLIER) cc_final: 0.3283 (pttt) outliers start: 9 outliers final: 4 residues processed: 122 average time/residue: 3.0558 time to fit residues: 405.2857 Evaluate side-chains 117 residues out of total 1427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 112 time to evaluate : 2.261 ------------------------------------------------------------------------------- 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 1078 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 157 optimal weight: 0.6980 chunk 129 optimal weight: 0.0030 chunk 144 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 overall best weight: 1.0394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 GLN A 208 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.0740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13304 Z= 0.173 Angle : 0.461 5.936 17978 Z= 0.238 Chirality : 0.036 0.141 1980 Planarity : 0.004 0.044 2325 Dihedral : 5.947 89.131 1784 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.42 % Allowed : 7.50 % Favored : 92.08 % 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: 0.95 (0.22), residues: 1596 helix: 1.67 (0.18), residues: 853 sheet: 0.70 (0.53), residues: 99 loop : -0.80 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 277 HIS 0.006 0.001 HIS C 409 PHE 0.020 0.001 PHE C 716 TYR 0.009 0.001 TYR A 599 ARG 0.008 0.000 ARG C 690 *********************** 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 122 residues out of total 1427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 116 time to evaluate : 2.231 Fit side-chains REVERT: A 821 PRO cc_start: 0.7892 (Cg_endo) cc_final: 0.7537 (Cg_exo) REVERT: B 37 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.8090 (mmp) REVERT: B 49 LEU cc_start: 0.6998 (tm) cc_final: 0.6509 (tm) REVERT: B 52 MET cc_start: 0.6799 (mtm) cc_final: 0.6474 (ptm) REVERT: B 75 ARG cc_start: 0.6753 (ttp-110) cc_final: 0.6159 (ttp-170) REVERT: B 84 GLU cc_start: 0.7018 (pm20) cc_final: 0.6718 (pm20) REVERT: B 138 ASN cc_start: 0.6031 (m110) cc_final: 0.5817 (t0) REVERT: C 291 MET cc_start: 0.8809 (mtp) cc_final: 0.8574 (mtp) REVERT: C 1078 LYS cc_start: 0.4420 (OUTLIER) cc_final: 0.3335 (pttt) outliers start: 6 outliers final: 3 residues processed: 120 average time/residue: 3.1508 time to fit residues: 412.4346 Evaluate side-chains 117 residues out of total 1427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 112 time to evaluate : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 143 optimal weight: 3.9990 chunk 109 optimal weight: 0.4980 chunk 75 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 146 optimal weight: 0.0980 chunk 154 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 138 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.0823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13304 Z= 0.199 Angle : 0.466 5.849 17978 Z= 0.240 Chirality : 0.037 0.138 1980 Planarity : 0.004 0.040 2325 Dihedral : 5.859 89.617 1784 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.63 % Allowed : 8.48 % Favored : 90.89 % 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: 0.98 (0.22), residues: 1596 helix: 1.70 (0.18), residues: 849 sheet: 0.72 (0.53), residues: 99 loop : -0.80 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 277 HIS 0.007 0.001 HIS C 409 PHE 0.020 0.001 PHE C 716 TYR 0.008 0.001 TYR A 301 ARG 0.004 0.000 ARG C 690 *********************** 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 124 residues out of total 1427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 115 time to evaluate : 1.958 Fit side-chains REVERT: A 821 PRO cc_start: 0.7891 (Cg_endo) cc_final: 0.7541 (Cg_exo) REVERT: B 49 LEU cc_start: 0.6912 (tm) cc_final: 0.6358 (tm) REVERT: B 52 MET cc_start: 0.6796 (mtm) cc_final: 0.6445 (ptm) REVERT: B 75 ARG cc_start: 0.6768 (ttp-110) cc_final: 0.6173 (ttp-170) REVERT: B 84 GLU cc_start: 0.7018 (pm20) cc_final: 0.6745 (pm20) REVERT: C 291 MET cc_start: 0.8791 (mtp) cc_final: 0.8563 (mtp) REVERT: C 1078 LYS cc_start: 0.4396 (OUTLIER) cc_final: 0.3310 (pttt) outliers start: 9 outliers final: 5 residues processed: 122 average time/residue: 2.9670 time to fit residues: 395.1423 Evaluate side-chains 117 residues out of total 1427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 111 time to evaluate : 2.041 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 138 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.0875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13304 Z= 0.207 Angle : 0.467 5.944 17978 Z= 0.242 Chirality : 0.037 0.139 1980 Planarity : 0.004 0.048 2325 Dihedral : 5.804 89.004 1784 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.63 % Allowed : 9.32 % Favored : 90.05 % 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: 1.01 (0.21), residues: 1596 helix: 1.71 (0.18), residues: 849 sheet: 0.72 (0.53), residues: 99 loop : -0.75 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 277 HIS 0.009 0.001 HIS C 409 PHE 0.020 0.001 PHE C 716 TYR 0.008 0.001 TYR A 301 ARG 0.005 0.000 ARG A 427 *********************** 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 fitting. rotamer outliers: 9 poor density : 118 time to evaluate : 2.096 Fit side-chains REVERT: A 205 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7527 (mppt) REVERT: A 821 PRO cc_start: 0.7882 (Cg_endo) cc_final: 0.7533 (Cg_exo) REVERT: B 49 LEU cc_start: 0.6971 (tm) cc_final: 0.6422 (tm) REVERT: B 52 MET cc_start: 0.6853 (mtm) cc_final: 0.6362 (ptm) REVERT: B 75 ARG cc_start: 0.6785 (ttp-110) cc_final: 0.6392 (tmm160) REVERT: B 84 GLU cc_start: 0.6972 (pm20) cc_final: 0.6706 (pm20) REVERT: C 291 MET cc_start: 0.8789 (mtp) cc_final: 0.8581 (mtp) REVERT: C 1078 LYS cc_start: 0.4380 (OUTLIER) cc_final: 0.3294 (pttt) outliers start: 9 outliers final: 5 residues processed: 124 average time/residue: 2.9852 time to fit residues: 404.4205 Evaluate side-chains 118 residues out of total 1427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 111 time to evaluate : 2.115 ------------------------------------------------------------------------------- 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 1078 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 38 optimal weight: 0.5980 chunk 154 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13304 Z= 0.220 Angle : 0.475 5.870 17978 Z= 0.246 Chirality : 0.037 0.138 1980 Planarity : 0.004 0.047 2325 Dihedral : 5.783 88.293 1784 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.70 % Allowed : 10.23 % Favored : 89.07 % 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: 1.02 (0.21), residues: 1596 helix: 1.74 (0.18), residues: 844 sheet: 0.71 (0.53), residues: 99 loop : -0.74 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 277 HIS 0.007 0.001 HIS C 409 PHE 0.020 0.001 PHE C 716 TYR 0.020 0.001 TYR C 246 ARG 0.005 0.000 ARG A 427 *********************** 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 123 residues out of total 1427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 113 time to evaluate : 2.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7530 (mppt) REVERT: A 821 PRO cc_start: 0.7888 (Cg_endo) cc_final: 0.7542 (Cg_exo) REVERT: B 49 LEU cc_start: 0.6999 (tm) cc_final: 0.6434 (tm) REVERT: B 52 MET cc_start: 0.6927 (mtm) cc_final: 0.6421 (ptm) REVERT: B 75 ARG cc_start: 0.6790 (ttp-110) cc_final: 0.6379 (tmm160) REVERT: B 84 GLU cc_start: 0.6941 (pm20) cc_final: 0.6677 (pm20) REVERT: C 1078 LYS cc_start: 0.4414 (OUTLIER) cc_final: 0.3334 (pttt) outliers start: 10 outliers final: 6 residues processed: 121 average time/residue: 2.9568 time to fit residues: 389.9609 Evaluate side-chains 117 residues out of total 1427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 109 time to evaluate : 2.016 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 154 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 94 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13304 Z= 0.277 Angle : 0.499 6.081 17978 Z= 0.260 Chirality : 0.038 0.146 1980 Planarity : 0.004 0.055 2325 Dihedral : 5.875 87.806 1784 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.70 % Allowed : 11.14 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.21), residues: 1596 helix: 1.62 (0.18), residues: 846 sheet: 0.65 (0.53), residues: 99 loop : -0.77 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 277 HIS 0.007 0.001 HIS C 409 PHE 0.021 0.002 PHE C 716 TYR 0.014 0.002 TYR C 246 ARG 0.005 0.000 ARG A 427 *********************** 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 119 residues out of total 1427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 2.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LYS cc_start: 0.7745 (OUTLIER) cc_final: 0.7507 (mppt) REVERT: A 821 PRO cc_start: 0.7888 (Cg_endo) cc_final: 0.7530 (Cg_exo) REVERT: B 84 GLU cc_start: 0.6923 (pm20) cc_final: 0.6676 (pm20) outliers start: 10 outliers final: 8 residues processed: 117 average time/residue: 3.0434 time to fit residues: 387.0904 Evaluate side-chains 114 residues out of total 1427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 105 time to evaluate : 1.965 ------------------------------------------------------------------------------- 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 1078 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 0.0370 chunk 29 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 overall best weight: 1.2062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13304 Z= 0.189 Angle : 0.472 5.828 17978 Z= 0.243 Chirality : 0.037 0.140 1980 Planarity : 0.004 0.051 2325 Dihedral : 5.749 87.458 1784 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.77 % Allowed : 11.28 % Favored : 87.95 % 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: 1.03 (0.21), residues: 1596 helix: 1.73 (0.18), residues: 850 sheet: 0.70 (0.53), residues: 99 loop : -0.74 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 277 HIS 0.006 0.001 HIS C 409 PHE 0.020 0.001 PHE C 716 TYR 0.012 0.001 TYR C 246 ARG 0.007 0.000 ARG A 427 *********************** 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 120 residues out of total 1427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 109 time to evaluate : 2.148 Fit side-chains REVERT: A 205 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7493 (mppt) REVERT: A 675 PHE cc_start: 0.8769 (OUTLIER) cc_final: 0.7952 (t80) REVERT: A 776 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7538 (mp0) REVERT: A 821 PRO cc_start: 0.7894 (Cg_endo) cc_final: 0.7548 (Cg_exo) REVERT: B 75 ARG cc_start: 0.6792 (ttp-110) cc_final: 0.6404 (tmm160) REVERT: B 84 GLU cc_start: 0.6916 (pm20) cc_final: 0.6591 (pm20) REVERT: C 1078 LYS cc_start: 0.4364 (OUTLIER) cc_final: 0.3278 (pttt) outliers start: 11 outliers final: 6 residues processed: 118 average time/residue: 3.0409 time to fit residues: 392.1454 Evaluate side-chains 116 residues out of total 1427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 106 time to evaluate : 2.133 ------------------------------------------------------------------------------- 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 A residue 776 GLU 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 140 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 134 optimal weight: 0.8980 chunk 143 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 129 optimal weight: 0.9990 chunk 135 optimal weight: 0.5980 chunk 94 optimal weight: 8.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13304 Z= 0.270 Angle : 0.498 5.937 17978 Z= 0.258 Chirality : 0.038 0.136 1980 Planarity : 0.004 0.055 2325 Dihedral : 5.848 87.237 1784 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.77 % Allowed : 11.21 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.21), residues: 1596 helix: 1.62 (0.18), residues: 847 sheet: 0.63 (0.53), residues: 99 loop : -0.76 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 277 HIS 0.006 0.001 HIS C 409 PHE 0.021 0.002 PHE C 716 TYR 0.017 0.002 TYR C 246 ARG 0.007 0.000 ARG A 427 *********************** 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 121 residues out of total 1427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 110 time to evaluate : 2.186 Fit side-chains revert: symmetry clash REVERT: A 205 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7500 (mppt) REVERT: A 675 PHE cc_start: 0.8822 (OUTLIER) cc_final: 0.8020 (t80) REVERT: A 776 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7583 (mp0) REVERT: A 821 PRO cc_start: 0.7897 (Cg_endo) cc_final: 0.7546 (Cg_exo) REVERT: B 84 GLU cc_start: 0.6910 (pm20) cc_final: 0.6605 (pm20) outliers start: 11 outliers final: 7 residues processed: 119 average time/residue: 3.0628 time to fit residues: 395.9760 Evaluate side-chains 117 residues out of total 1427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 107 time to evaluate : 1.940 ------------------------------------------------------------------------------- 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 A residue 776 GLU 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 151 optimal weight: 0.4980 chunk 92 optimal weight: 4.9990 chunk 72 optimal weight: 0.3980 chunk 105 optimal weight: 1.9990 chunk 159 optimal weight: 0.0980 chunk 146 optimal weight: 0.0670 chunk 126 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13304 Z= 0.143 Angle : 0.455 5.821 17978 Z= 0.233 Chirality : 0.036 0.143 1980 Planarity : 0.004 0.055 2325 Dihedral : 5.593 86.855 1784 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.56 % Allowed : 11.63 % Favored : 87.81 % 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: 1.19 (0.22), residues: 1596 helix: 1.88 (0.18), residues: 852 sheet: 0.72 (0.53), residues: 99 loop : -0.67 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 277 HIS 0.006 0.001 HIS C 409 PHE 0.029 0.001 PHE A 425 TYR 0.016 0.001 TYR C 246 ARG 0.008 0.000 ARG A 427 ********************** 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 124 residues out of total 1427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 116 time to evaluate : 1.898 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 776 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7608 (mp0) REVERT: A 821 PRO cc_start: 0.7886 (Cg_endo) cc_final: 0.7555 (Cg_exo) REVERT: B 75 ARG cc_start: 0.6749 (ttp-110) cc_final: 0.6145 (ttp-170) REVERT: B 84 GLU cc_start: 0.6903 (pm20) cc_final: 0.6577 (pm20) REVERT: C 1078 LYS cc_start: 0.4314 (OUTLIER) cc_final: 0.3232 (pttt) outliers start: 8 outliers final: 5 residues processed: 122 average time/residue: 2.9191 time to fit residues: 388.8285 Evaluate side-chains 117 residues out of total 1427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 110 time to evaluate : 2.116 ------------------------------------------------------------------------------- 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 A residue 776 GLU 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 135 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 0.3980 chunk 111 optimal weight: 0.8980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.136411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.098802 restraints weight = 54221.359| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.10 r_work: 0.3065 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13304 Z= 0.223 Angle : 0.479 6.061 17978 Z= 0.247 Chirality : 0.037 0.138 1980 Planarity : 0.004 0.058 2325 Dihedral : 5.714 86.928 1784 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.56 % Allowed : 11.63 % Favored : 87.81 % 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: 1.09 (0.22), residues: 1596 helix: 1.78 (0.18), residues: 852 sheet: 0.67 (0.53), residues: 99 loop : -0.70 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 277 HIS 0.005 0.001 HIS C 409 PHE 0.026 0.001 PHE A 425 TYR 0.008 0.001 TYR A 301 ARG 0.008 0.000 ARG A 427 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8512.54 seconds wall clock time: 150 minutes 29.42 seconds (9029.42 seconds total)