Starting phenix.real_space_refine (version: dev) on Sat Feb 25 17:38:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mis_23863/02_2023/7mis_23863_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mis_23863/02_2023/7mis_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_2023/7mis_23863.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mis_23863/02_2023/7mis_23863.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mis_23863/02_2023/7mis_23863_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mis_23863/02_2023/7mis_23863_trim_updated.pdb" } 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 ------------------------------------------------------------------------------- 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 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 11.26, per 1000 atoms: 0.43 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: 23.16 Conformation dependent library (CDL) restraints added in 2.2 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: 2.07 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: 9.46 Time building geometry restraints manager: 23.56 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: 10211 28.33 - 56.66: 277 56.66 - 84.99: 34 84.99 - 113.32: 3 113.32 - 141.65: 1 Dihedral angle restraints: 10526 sinusoidal: 4962 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 10523 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 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. 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: 2.970 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: 0.370 Extract box with map and model: 15.680 Check model and map are aligned: 0.360 Process input model: 80.330 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.210 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:12.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.890 ------------------------------------------------------------------------------- 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 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 : 14.511 141.649 5027 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 % 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 *********************** 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 : 2.238 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 3.1635 time to fit residues: 554.7205 Evaluate side-chains 110 residues out of total 1427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 2.327 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2761 ------------------------------------------------------------------------------- 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: 3.9990 chunk 67 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 64 optimal weight: 0.8980 chunk 125 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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: 0.8081 moved from start: 0.0812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 13304 Z= 0.320 Angle : 0.524 7.162 17978 Z= 0.274 Chirality : 0.039 0.142 1980 Planarity : 0.004 0.052 2325 Dihedral : 5.423 82.769 1753 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer Outliers : 0.77 % 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: 0.63 (0.21), residues: 1596 helix: 1.41 (0.18), residues: 848 sheet: 0.60 (0.52), residues: 99 loop : -0.93 (0.24), residues: 649 *********************** 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 fitting. rotamer outliers: 11 poor density : 116 time to evaluate : 2.209 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 123 average time/residue: 3.2384 time to fit residues: 433.5131 Evaluate side-chains 115 residues out of total 1427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 111 time to evaluate : 2.340 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 2.9068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 40 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 157 optimal weight: 6.9990 chunk 129 optimal weight: 0.0000 chunk 144 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 overall best weight: 1.5790 ------------------------------------------------------------------------------- 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: 0.8070 moved from start: 0.0836 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= 0.226 Angle : 0.489 5.894 17978 Z= 0.253 Chirality : 0.037 0.138 1980 Planarity : 0.004 0.043 2325 Dihedral : 5.277 74.632 1753 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer Outliers : 0.56 % 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: 0.74 (0.21), residues: 1596 helix: 1.48 (0.18), residues: 852 sheet: 0.61 (0.52), residues: 99 loop : -0.87 (0.24), residues: 645 *********************** 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 123 residues out of total 1427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 115 time to evaluate : 2.165 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 121 average time/residue: 3.0648 time to fit residues: 403.9739 Evaluate side-chains 117 residues out of total 1427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 112 time to evaluate : 2.199 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 3.1872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 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: 2.9990 chunk 154 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 138 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS B 112 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 13304 Z= 0.231 Angle : 0.486 5.986 17978 Z= 0.252 Chirality : 0.037 0.138 1980 Planarity : 0.004 0.041 2325 Dihedral : 5.196 68.283 1753 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.21), residues: 1596 helix: 1.57 (0.18), residues: 845 sheet: 0.62 (0.53), residues: 99 loop : -0.82 (0.25), residues: 652 *********************** 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 125 residues out of total 1427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 113 time to evaluate : 2.279 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 123 average time/residue: 2.9463 time to fit residues: 396.7410 Evaluate side-chains 117 residues out of total 1427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 111 time to evaluate : 2.159 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 1.6520 time to fit residues: 4.7096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 115 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 138 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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: 0.8082 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 13304 Z= 0.274 Angle : 0.503 6.063 17978 Z= 0.261 Chirality : 0.038 0.137 1980 Planarity : 0.004 0.046 2325 Dihedral : 5.228 66.945 1753 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer Outliers : 0.70 % 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: 0.74 (0.21), residues: 1596 helix: 1.50 (0.18), residues: 845 sheet: 0.59 (0.52), residues: 99 loop : -0.86 (0.24), residues: 652 *********************** 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 126 residues out of total 1427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 116 time to evaluate : 2.073 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 125 average time/residue: 2.9915 time to fit residues: 410.1095 Evaluate side-chains 117 residues out of total 1427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 110 time to evaluate : 2.363 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 1.8172 time to fit residues: 5.1184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 154 optimal weight: 8.9990 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: 4.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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: 0.8071 moved from start: 0.1019 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= 0.208 Angle : 0.482 5.954 17978 Z= 0.249 Chirality : 0.037 0.149 1980 Planarity : 0.004 0.050 2325 Dihedral : 5.131 64.721 1753 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer Outliers : 0.77 % 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: 0.90 (0.21), residues: 1596 helix: 1.64 (0.18), residues: 844 sheet: 0.62 (0.53), residues: 99 loop : -0.79 (0.25), residues: 653 *********************** 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 127 residues out of total 1427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 116 time to evaluate : 2.082 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 126 average time/residue: 2.9115 time to fit residues: 401.5750 Evaluate side-chains 119 residues out of total 1427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 113 time to evaluate : 2.348 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 3.0363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 113 optimal weight: 0.4980 chunk 87 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 86 optimal weight: 9.9990 chunk 154 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 chunk 94 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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: 0.8078 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 13304 Z= 0.242 Angle : 0.493 5.872 17978 Z= 0.255 Chirality : 0.038 0.138 1980 Planarity : 0.004 0.053 2325 Dihedral : 5.149 63.946 1753 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer Outliers : 0.63 % 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: 0.86 (0.21), residues: 1596 helix: 1.59 (0.18), residues: 846 sheet: 0.59 (0.52), residues: 99 loop : -0.79 (0.25), residues: 651 *********************** 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 122 residues out of total 1427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 113 time to evaluate : 2.251 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 120 average time/residue: 3.0418 time to fit residues: 397.9658 Evaluate side-chains 116 residues out of total 1427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 110 time to evaluate : 2.273 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 2.9147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 92 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 chunk 105 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 121 optimal weight: 0.0370 overall best weight: 0.9862 ------------------------------------------------------------------------------- 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: 0.8063 moved from start: 0.1066 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= 0.167 Angle : 0.468 5.705 17978 Z= 0.240 Chirality : 0.036 0.141 1980 Planarity : 0.003 0.052 2325 Dihedral : 5.013 63.600 1753 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer Outliers : 0.70 % 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: 1.05 (0.22), residues: 1596 helix: 1.74 (0.18), residues: 852 sheet: 0.65 (0.53), residues: 99 loop : -0.71 (0.25), residues: 645 *********************** 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 122 residues out of total 1427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 112 time to evaluate : 2.218 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 121 average time/residue: 2.9885 time to fit residues: 394.3560 Evaluate side-chains 119 residues out of total 1427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 113 time to evaluate : 2.342 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 3.0753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 134 optimal weight: 0.6980 chunk 143 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 135 optimal weight: 0.6980 chunk 94 optimal weight: 7.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- 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: 0.8098 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 : 0.006 0.052 13304 Z= 0.372 Angle : 0.549 6.287 17978 Z= 0.288 Chirality : 0.040 0.136 1980 Planarity : 0.004 0.058 2325 Dihedral : 5.305 64.172 1753 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer Outliers : 0.70 % 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: 0.63 (0.21), residues: 1596 helix: 1.40 (0.18), residues: 846 sheet: 0.50 (0.52), residues: 99 loop : -0.89 (0.24), residues: 651 *********************** 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 122 residues out of total 1427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 112 time to evaluate : 2.137 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 122 average time/residue: 3.1118 time to fit residues: 413.6355 Evaluate side-chains 118 residues out of total 1427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 112 time to evaluate : 2.267 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 2.9849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 105 optimal weight: 0.0970 chunk 159 optimal weight: 0.0060 chunk 146 optimal weight: 0.1980 chunk 126 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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: 0.8060 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 13304 Z= 0.145 Angle : 0.468 5.921 17978 Z= 0.241 Chirality : 0.036 0.143 1980 Planarity : 0.003 0.056 2325 Dihedral : 4.993 60.643 1753 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer Outliers : 0.49 % 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: 1.05 (0.22), residues: 1596 helix: 1.73 (0.18), residues: 853 sheet: 0.64 (0.53), residues: 99 loop : -0.70 (0.25), residues: 644 ********************** 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 122 residues out of total 1427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 115 time to evaluate : 2.389 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 7 residues processed: 122 average time/residue: 3.0637 time to fit residues: 407.7996 Evaluate side-chains 120 residues out of total 1427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 113 time to evaluate : 2.384 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 6.1907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 53 optimal weight: 0.5980 chunk 130 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.136377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.099706 restraints weight = 54116.966| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.06 r_work: 0.3064 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1090 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= 0.203 Angle : 0.477 5.791 17978 Z= 0.246 Chirality : 0.037 0.139 1980 Planarity : 0.003 0.042 2325 Dihedral : 5.032 63.312 1753 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer Outliers : 0.56 % 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: 1.04 (0.22), residues: 1596 helix: 1.72 (0.18), residues: 853 sheet: 0.66 (0.53), residues: 99 loop : -0.71 (0.25), residues: 644 =============================================================================== Job complete usr+sys time: 8398.29 seconds wall clock time: 148 minutes 54.84 seconds (8934.84 seconds total)