Starting phenix.real_space_refine on Wed Feb 21 17:07:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9g_14572/02_2024/7z9g_14572_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9g_14572/02_2024/7z9g_14572.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9g_14572/02_2024/7z9g_14572_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9g_14572/02_2024/7z9g_14572_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9g_14572/02_2024/7z9g_14572_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9g_14572/02_2024/7z9g_14572.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9g_14572/02_2024/7z9g_14572.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9g_14572/02_2024/7z9g_14572_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9g_14572/02_2024/7z9g_14572_trim_updated.pdb" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 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: 7 Type Number sf(0) Gaussians P 64 5.49 5 Mg 2 5.21 5 S 58 5.16 5 C 9825 2.51 5 N 2839 2.21 5 O 3184 1.98 5 H 15363 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 31335 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 8208 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 21, 'TRANS': 495} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 6406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 6406 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 15, 'TRANS': 386} Chain: "C" Number of atoms: 8208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 8208 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 21, 'TRANS': 495} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 6406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 6406 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 15, 'TRANS': 386} Chain: "E" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 450 Classifications: {'DNA': 14} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 13} Chain: "F" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 448 Classifications: {'DNA': 14} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 13} Chain: "G" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 561 Classifications: {'DNA': 18} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 17} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 568 Classifications: {'DNA': 18} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 17} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 68 Unusual residues: {'IM0': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 14.15, per 1000 atoms: 0.45 Number of scatterers: 31335 At special positions: 0 Unit cell: (129, 135.88, 138.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 58 16.00 P 64 15.00 Mg 2 11.99 O 3184 8.00 N 2839 7.00 C 9825 6.00 H 15363 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 24.79 Conformation dependent library (CDL) restraints added in 2.9 seconds 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3440 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 71 helices and 20 sheets defined 44.3% alpha, 8.7% beta 6 base pairs and 51 stacking pairs defined. Time for finding SS restraints: 15.67 Creating SS restraints... Processing helix chain 'A' and resid 13 through 29 Processing helix chain 'A' and resid 43 through 54 Processing helix chain 'A' and resid 66 through 76 Processing helix chain 'A' and resid 82 through 93 removed outlier: 3.631A pdb=" N MET A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA A 93 " --> pdb=" O ILE A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 134 Processing helix chain 'A' and resid 165 through 169 Processing helix chain 'A' and resid 187 through 199 Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 227 through 235 Processing helix chain 'A' and resid 270 through 282 Processing helix chain 'A' and resid 313 through 323 Processing helix chain 'A' and resid 347 through 388 removed outlier: 3.586A pdb=" N ALA A 382 " --> pdb=" O HIS A 378 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 399 Processing helix chain 'A' and resid 403 through 412 Processing helix chain 'A' and resid 418 through 426 removed outlier: 3.891A pdb=" N ALA A 421 " --> pdb=" O GLY A 418 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ALA A 422 " --> pdb=" O ASN A 419 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET A 423 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU A 424 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU A 425 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 459 Processing helix chain 'A' and resid 463 through 466 Processing helix chain 'A' and resid 468 through 493 removed outlier: 3.695A pdb=" N LEU A 474 " --> pdb=" O GLU A 470 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU A 475 " --> pdb=" O HIS A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 513 Processing helix chain 'B' and resid 427 through 435 Processing helix chain 'B' and resid 458 through 463 removed outlier: 3.941A pdb=" N LEU B 462 " --> pdb=" O PHE B 458 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER B 463 " --> pdb=" O ASP B 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 458 through 463' Processing helix chain 'B' and resid 465 through 474 Processing helix chain 'B' and resid 501 through 517 Processing helix chain 'B' and resid 519 through 524 Processing helix chain 'B' and resid 549 through 560 Processing helix chain 'B' and resid 578 through 596 Processing helix chain 'B' and resid 603 through 609 Processing helix chain 'B' and resid 626 through 638 removed outlier: 3.807A pdb=" N VAL B 630 " --> pdb=" O VAL B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 682 No H-bonds generated for 'chain 'B' and resid 679 through 682' Processing helix chain 'B' and resid 685 through 696 removed outlier: 3.894A pdb=" N LYS B 696 " --> pdb=" O THR B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 733 removed outlier: 4.892A pdb=" N GLY B 733 " --> pdb=" O GLU B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 744 No H-bonds generated for 'chain 'B' and resid 742 through 744' Processing helix chain 'B' and resid 747 through 753 Processing helix chain 'B' and resid 770 through 781 Processing helix chain 'B' and resid 785 through 794 Processing helix chain 'B' and resid 797 through 800 No H-bonds generated for 'chain 'B' and resid 797 through 800' Processing helix chain 'C' and resid 13 through 31 Processing helix chain 'C' and resid 43 through 54 Processing helix chain 'C' and resid 66 through 76 Processing helix chain 'C' and resid 82 through 93 removed outlier: 3.551A pdb=" N MET C 92 " --> pdb=" O THR C 88 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA C 93 " --> pdb=" O ILE C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 134 Processing helix chain 'C' and resid 165 through 169 Processing helix chain 'C' and resid 187 through 199 Processing helix chain 'C' and resid 205 through 209 Processing helix chain 'C' and resid 227 through 235 Processing helix chain 'C' and resid 270 through 282 Processing helix chain 'C' and resid 313 through 323 Processing helix chain 'C' and resid 347 through 399 removed outlier: 3.632A pdb=" N ILE C 379 " --> pdb=" O ASP C 375 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN C 389 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE C 390 " --> pdb=" O ALA C 386 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ASP C 391 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Proline residue: C 392 - end of helix removed outlier: 3.768A pdb=" N HIS C 399 " --> pdb=" O GLU C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 411 Processing helix chain 'C' and resid 418 through 427 removed outlier: 3.736A pdb=" N ALA C 421 " --> pdb=" O GLY C 418 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA C 422 " --> pdb=" O ASN C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 459 Processing helix chain 'C' and resid 463 through 466 Processing helix chain 'C' and resid 468 through 492 removed outlier: 3.718A pdb=" N LEU C 474 " --> pdb=" O GLU C 470 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU C 475 " --> pdb=" O HIS C 471 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP C 483 " --> pdb=" O LYS C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 513 Processing helix chain 'D' and resid 426 through 434 removed outlier: 3.682A pdb=" N GLN D 434 " --> pdb=" O GLY D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 463 Processing helix chain 'D' and resid 465 through 474 Processing helix chain 'D' and resid 501 through 517 Processing helix chain 'D' and resid 519 through 524 Processing helix chain 'D' and resid 550 through 560 Processing helix chain 'D' and resid 578 through 596 removed outlier: 3.635A pdb=" N ARG D 596 " --> pdb=" O LYS D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 603 through 610 removed outlier: 4.167A pdb=" N ILE D 610 " --> pdb=" O LEU D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 617 through 620 No H-bonds generated for 'chain 'D' and resid 617 through 620' Processing helix chain 'D' and resid 626 through 639 Processing helix chain 'D' and resid 679 through 683 Processing helix chain 'D' and resid 685 through 696 removed outlier: 3.536A pdb=" N LYS D 696 " --> pdb=" O THR D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 719 through 731 Processing helix chain 'D' and resid 742 through 744 No H-bonds generated for 'chain 'D' and resid 742 through 744' Processing helix chain 'D' and resid 747 through 754 Processing helix chain 'D' and resid 770 through 781 Processing helix chain 'D' and resid 785 through 794 Processing sheet with id= A, first strand: chain 'A' and resid 103 through 106 Processing sheet with id= B, first strand: chain 'A' and resid 145 through 147 Processing sheet with id= C, first strand: chain 'A' and resid 171 through 174 Processing sheet with id= D, first strand: chain 'A' and resid 222 through 224 removed outlier: 6.783A pdb=" N GLU A 520 " --> pdb=" O ILE A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 237 through 243 Processing sheet with id= F, first strand: chain 'A' and resid 245 through 250 removed outlier: 3.731A pdb=" N GLU A 263 " --> pdb=" O ARG A 245 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N GLU A 247 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N VAL A 261 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N GLU A 249 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ILE A 259 " --> pdb=" O GLU A 249 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N GLU A 257 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL A 307 " --> pdb=" O GLU A 257 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 335 through 337 Processing sheet with id= H, first strand: chain 'B' and resid 419 through 421 removed outlier: 6.739A pdb=" N SER B 492 " --> pdb=" O LEU B 420 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 542 through 546 removed outlier: 3.829A pdb=" N GLN B 542 " --> pdb=" O LYS B 539 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 646 through 648 Processing sheet with id= K, first strand: chain 'B' and resid 651 through 653 Processing sheet with id= L, first strand: chain 'C' and resid 103 through 106 Processing sheet with id= M, first strand: chain 'C' and resid 145 through 147 Processing sheet with id= N, first strand: chain 'C' and resid 171 through 174 Processing sheet with id= O, first strand: chain 'C' and resid 520 through 522 removed outlier: 4.032A pdb=" N TYR C 241 " --> pdb=" O ASN C 224 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 246 through 249 Processing sheet with id= Q, first strand: chain 'C' and resid 335 through 337 Processing sheet with id= R, first strand: chain 'D' and resid 528 through 530 Processing sheet with id= S, first strand: chain 'D' and resid 543 through 546 Processing sheet with id= T, first strand: chain 'D' and resid 646 through 652 601 hydrogen bonds defined for protein. 1713 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 13 hydrogen bonds 26 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 51 stacking parallelities Total time for adding SS restraints: 12.31 Time building geometry restraints manager: 25.45 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: 15355 1.03 - 1.23: 36 1.23 - 1.42: 6711 1.42 - 1.61: 9513 1.61 - 1.81: 108 Bond restraints: 31723 Sorted by residual: bond pdb=" OH PTR C 122 " pdb=" P PTR C 122 " ideal model delta sigma weight residual 1.769 1.609 0.160 2.00e-02 2.50e+03 6.36e+01 bond pdb=" OH PTR A 122 " pdb=" P PTR A 122 " ideal model delta sigma weight residual 1.769 1.612 0.157 2.00e-02 2.50e+03 6.15e+01 bond pdb=" C11 IM0 C 901 " pdb=" N1 IM0 C 901 " ideal model delta sigma weight residual 1.475 1.342 0.133 2.00e-02 2.50e+03 4.42e+01 bond pdb=" C16 IM0 C 901 " pdb=" N5 IM0 C 901 " ideal model delta sigma weight residual 1.481 1.351 0.130 2.00e-02 2.50e+03 4.20e+01 bond pdb=" C21 IM0 C 901 " pdb=" N6 IM0 C 901 " ideal model delta sigma weight residual 1.482 1.356 0.126 2.00e-02 2.50e+03 3.99e+01 ... (remaining 31718 not shown) Histogram of bond angle deviations from ideal: 100.36 - 107.10: 1313 107.10 - 113.84: 37535 113.84 - 120.57: 10542 120.57 - 127.31: 7815 127.31 - 134.05: 252 Bond angle restraints: 57457 Sorted by residual: angle pdb=" C32 IM0 C 901 " pdb=" C33 IM0 C 901 " pdb=" O4 IM0 C 901 " ideal model delta sigma weight residual 63.72 119.31 -55.59 3.00e+00 1.11e-01 3.43e+02 angle pdb=" C27 IM0 C 901 " pdb=" C33 IM0 C 901 " pdb=" O4 IM0 C 901 " ideal model delta sigma weight residual 157.05 117.66 39.39 3.00e+00 1.11e-01 1.72e+02 angle pdb=" C35 IM0 C 901 " pdb=" C36 IM0 C 901 " pdb=" O7 IM0 C 901 " ideal model delta sigma weight residual 92.39 121.18 -28.79 3.00e+00 1.11e-01 9.21e+01 angle pdb=" C22 IM0 C 901 " pdb=" C36 IM0 C 901 " pdb=" O7 IM0 C 901 " ideal model delta sigma weight residual 146.34 118.74 27.60 3.00e+00 1.11e-01 8.46e+01 angle pdb=" C36 IM0 C 901 " pdb=" C22 IM0 C 901 " pdb=" N6 IM0 C 901 " ideal model delta sigma weight residual 93.26 117.36 -24.10 3.00e+00 1.11e-01 6.45e+01 ... (remaining 57452 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.76: 13810 26.76 - 53.53: 544 53.53 - 80.29: 109 80.29 - 107.05: 3 107.05 - 133.82: 2 Dihedral angle restraints: 14468 sinusoidal: 8494 harmonic: 5974 Sorted by residual: dihedral pdb=" CA ARG A 32 " pdb=" C ARG A 32 " pdb=" N ALA A 33 " pdb=" CA ALA A 33 " ideal model delta harmonic sigma weight residual -180.00 -159.25 -20.75 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA GLY D 577 " pdb=" C GLY D 577 " pdb=" N GLU D 578 " pdb=" CA GLU D 578 " ideal model delta harmonic sigma weight residual 180.00 -160.21 -19.79 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA ASP B 674 " pdb=" C ASP B 674 " pdb=" N TYR B 675 " pdb=" CA TYR B 675 " ideal model delta harmonic sigma weight residual 180.00 161.76 18.24 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 14465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1666 0.033 - 0.067: 597 0.067 - 0.100: 135 0.100 - 0.133: 92 0.133 - 0.166: 13 Chirality restraints: 2503 Sorted by residual: chirality pdb=" CA ILE C 182 " pdb=" N ILE C 182 " pdb=" C ILE C 182 " pdb=" CB ILE C 182 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.92e-01 chirality pdb=" CA ILE A 182 " pdb=" N ILE A 182 " pdb=" C ILE A 182 " pdb=" CB ILE A 182 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.78e-01 chirality pdb=" CA ILE A 163 " pdb=" N ILE A 163 " pdb=" C ILE A 163 " pdb=" CB ILE A 163 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.76e-01 ... (remaining 2500 not shown) Planarity restraints: 4515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C27 IM0 C 901 " -0.050 2.00e-02 2.50e+03 8.64e-02 1.86e+02 pdb=" C28 IM0 C 901 " 0.013 2.00e-02 2.50e+03 pdb=" C29 IM0 C 901 " 0.044 2.00e-02 2.50e+03 pdb=" C30 IM0 C 901 " 0.013 2.00e-02 2.50e+03 pdb=" C31 IM0 C 901 " 0.061 2.00e-02 2.50e+03 pdb=" C32 IM0 C 901 " -0.060 2.00e-02 2.50e+03 pdb=" C33 IM0 C 901 " -0.095 2.00e-02 2.50e+03 pdb=" N7 IM0 C 901 " -0.038 2.00e-02 2.50e+03 pdb=" O3 IM0 C 901 " -0.095 2.00e-02 2.50e+03 pdb=" O4 IM0 C 901 " 0.207 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PTR A 122 " -0.036 2.00e-02 2.50e+03 7.15e-02 5.11e+01 pdb=" C PTR A 122 " 0.124 2.00e-02 2.50e+03 pdb=" O PTR A 122 " -0.046 2.00e-02 2.50e+03 pdb=" N THR A 123 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 IM0 C 901 " -0.058 2.00e-02 2.50e+03 6.34e-02 5.03e+01 pdb=" C11 IM0 C 901 " 0.019 2.00e-02 2.50e+03 pdb=" C12 IM0 C 901 " -0.077 2.00e-02 2.50e+03 pdb=" N1 IM0 C 901 " 0.101 2.00e-02 2.50e+03 pdb=" O10 IM0 C 901 " 0.015 2.00e-02 2.50e+03 ... (remaining 4512 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 6379 2.32 - 2.89: 69335 2.89 - 3.46: 71410 3.46 - 4.03: 99465 4.03 - 4.60: 153858 Nonbonded interactions: 400447 Sorted by model distance: nonbonded pdb=" HE ARG C 121 " pdb=" O1P PTR C 122 " model vdw 1.750 1.850 nonbonded pdb=" OD1 ASN A 165 " pdb="HD21 ASN A 169 " model vdw 1.753 1.850 nonbonded pdb=" OE1 GLU B 720 " pdb=" H GLU B 720 " model vdw 1.760 1.850 nonbonded pdb=" O GLU A 314 " pdb="HD21 ASN A 318 " model vdw 1.760 1.850 nonbonded pdb=" OE1 GLN B 646 " pdb="HH21 ARG B 665 " model vdw 1.760 1.850 ... (remaining 400442 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and resid 8 through 524) } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 3.230 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: 0.470 Extract box with map and model: 14.670 Check model and map are aligned: 0.450 Set scattering table: 0.290 Process input model: 107.410 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 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 : 0.005 0.160 16360 Z= 0.303 Angle : 0.855 55.588 22392 Z= 0.373 Chirality : 0.041 0.166 2503 Planarity : 0.004 0.086 2710 Dihedral : 13.202 133.816 6396 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.13 % Allowed : 2.13 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.20), residues: 1824 helix: 2.46 (0.18), residues: 833 sheet: 0.04 (0.38), residues: 184 loop : -1.55 (0.20), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 751 HIS 0.003 0.001 HIS C 339 PHE 0.006 0.001 PHE C 330 TYR 0.011 0.001 TYR A 266 ARG 0.002 0.000 ARG C 47 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 264 time to evaluate : 2.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 415 PRO cc_start: 0.7086 (Cg_endo) cc_final: 0.6705 (Cg_exo) REVERT: D 552 MET cc_start: 0.8057 (tpt) cc_final: 0.7721 (tpt) outliers start: 2 outliers final: 1 residues processed: 265 average time/residue: 0.8536 time to fit residues: 305.5724 Evaluate side-chains 143 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 142 time to evaluate : 2.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 708 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 95 optimal weight: 0.4980 chunk 75 optimal weight: 10.0000 chunk 145 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 168 optimal weight: 0.0970 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 HIS B 721 GLN C 45 HIS ** D 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16360 Z= 0.196 Angle : 0.487 10.840 22392 Z= 0.267 Chirality : 0.039 0.144 2503 Planarity : 0.004 0.038 2710 Dihedral : 15.519 138.211 2747 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.77 % Allowed : 5.74 % Favored : 93.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.20), residues: 1824 helix: 2.76 (0.18), residues: 826 sheet: 0.01 (0.38), residues: 185 loop : -1.53 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 629 HIS 0.009 0.001 HIS B 679 PHE 0.008 0.001 PHE B 681 TYR 0.011 0.001 TYR C 266 ARG 0.003 0.000 ARG B 438 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 145 time to evaluate : 2.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 415 PRO cc_start: 0.7226 (Cg_endo) cc_final: 0.6836 (Cg_exo) REVERT: D 552 MET cc_start: 0.8213 (tpt) cc_final: 0.7580 (tpt) outliers start: 12 outliers final: 10 residues processed: 154 average time/residue: 0.7253 time to fit residues: 161.1605 Evaluate side-chains 144 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 134 time to evaluate : 2.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain D residue 708 GLU Chi-restraints excluded: chain D residue 734 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 115 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 167 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 135 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 HIS ** D 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16360 Z= 0.181 Angle : 0.471 10.647 22392 Z= 0.259 Chirality : 0.039 0.144 2503 Planarity : 0.004 0.037 2710 Dihedral : 15.692 139.803 2747 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.65 % Allowed : 6.13 % Favored : 93.23 % 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: 0.99 (0.20), residues: 1824 helix: 2.75 (0.18), residues: 825 sheet: 0.02 (0.38), residues: 185 loop : -1.52 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 629 HIS 0.006 0.001 HIS B 679 PHE 0.006 0.001 PHE D 719 TYR 0.011 0.001 TYR C 266 ARG 0.002 0.000 ARG C 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 141 time to evaluate : 2.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 415 PRO cc_start: 0.7202 (Cg_endo) cc_final: 0.6823 (Cg_exo) REVERT: D 552 MET cc_start: 0.8260 (tpt) cc_final: 0.7626 (tpt) outliers start: 10 outliers final: 9 residues processed: 147 average time/residue: 0.7133 time to fit residues: 149.9995 Evaluate side-chains 141 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 132 time to evaluate : 2.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 346 ASN Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain D residue 734 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 9.9990 chunk 127 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 169 optimal weight: 0.7980 chunk 179 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 160 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 HIS ** D 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16360 Z= 0.210 Angle : 0.481 10.197 22392 Z= 0.265 Chirality : 0.040 0.145 2503 Planarity : 0.004 0.037 2710 Dihedral : 15.834 138.840 2744 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.84 % Allowed : 6.84 % Favored : 92.32 % 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 (0.20), residues: 1824 helix: 2.70 (0.18), residues: 825 sheet: 0.03 (0.38), residues: 184 loop : -1.60 (0.20), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 629 HIS 0.004 0.001 HIS B 679 PHE 0.009 0.001 PHE B 719 TYR 0.012 0.001 TYR C 266 ARG 0.002 0.000 ARG C 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 136 time to evaluate : 2.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 145 average time/residue: 0.7040 time to fit residues: 149.2140 Evaluate side-chains 141 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 131 time to evaluate : 2.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain D residue 598 GLU Chi-restraints excluded: chain D residue 734 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 133 optimal weight: 2.9990 chunk 74 optimal weight: 0.0050 chunk 153 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS A 471 HIS D 569 ASN ** D 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16360 Z= 0.181 Angle : 0.464 10.255 22392 Z= 0.256 Chirality : 0.039 0.144 2503 Planarity : 0.004 0.036 2710 Dihedral : 15.861 140.997 2744 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.90 % Allowed : 7.35 % Favored : 91.74 % 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 (0.20), residues: 1824 helix: 2.78 (0.18), residues: 819 sheet: -0.02 (0.37), residues: 185 loop : -1.53 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 629 HIS 0.003 0.001 HIS B 679 PHE 0.007 0.001 PHE B 719 TYR 0.010 0.001 TYR C 266 ARG 0.002 0.000 ARG C 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 136 time to evaluate : 2.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 552 MET cc_start: 0.8359 (tpt) cc_final: 0.7698 (tpt) outliers start: 14 outliers final: 13 residues processed: 145 average time/residue: 0.7275 time to fit residues: 150.8522 Evaluate side-chains 145 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 132 time to evaluate : 2.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 346 ASN Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain D residue 481 ASP Chi-restraints excluded: chain D residue 598 GLU Chi-restraints excluded: chain D residue 734 LEU Chi-restraints excluded: chain D residue 794 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 105 optimal weight: 0.3980 chunk 44 optimal weight: 0.7980 chunk 179 optimal weight: 1.9990 chunk 149 optimal weight: 0.0270 chunk 83 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.0442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 HIS ** D 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16360 Z= 0.176 Angle : 0.459 10.164 22392 Z= 0.253 Chirality : 0.039 0.145 2503 Planarity : 0.004 0.036 2710 Dihedral : 15.896 140.756 2744 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.84 % Allowed : 7.74 % Favored : 91.42 % 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 (0.20), residues: 1824 helix: 2.77 (0.18), residues: 822 sheet: 0.02 (0.37), residues: 185 loop : -1.51 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 629 HIS 0.003 0.001 HIS B 679 PHE 0.007 0.001 PHE B 719 TYR 0.012 0.001 TYR B 555 ARG 0.003 0.000 ARG B 600 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 138 time to evaluate : 2.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 552 MET cc_start: 0.8348 (tpt) cc_final: 0.7685 (tpt) outliers start: 13 outliers final: 13 residues processed: 148 average time/residue: 0.7177 time to fit residues: 152.0075 Evaluate side-chains 145 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 132 time to evaluate : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 346 ASN Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 346 ASN Chi-restraints excluded: chain D residue 481 ASP Chi-restraints excluded: chain D residue 598 GLU Chi-restraints excluded: chain D residue 734 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 179 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 HIS A 524 ASN ** D 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16360 Z= 0.250 Angle : 0.496 10.280 22392 Z= 0.274 Chirality : 0.040 0.154 2503 Planarity : 0.004 0.035 2710 Dihedral : 16.064 140.987 2744 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.03 % Allowed : 7.94 % Favored : 91.03 % 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: 0.82 (0.20), residues: 1824 helix: 2.63 (0.18), residues: 822 sheet: 0.02 (0.38), residues: 185 loop : -1.64 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 415 HIS 0.003 0.001 HIS C 78 PHE 0.009 0.001 PHE A 368 TYR 0.012 0.001 TYR C 266 ARG 0.004 0.000 ARG C 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 138 time to evaluate : 2.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 552 MET cc_start: 0.8337 (tpt) cc_final: 0.7664 (tpt) outliers start: 16 outliers final: 14 residues processed: 150 average time/residue: 0.6821 time to fit residues: 149.0857 Evaluate side-chains 149 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 135 time to evaluate : 2.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 346 ASN Chi-restraints excluded: chain D residue 481 ASP Chi-restraints excluded: chain D residue 734 LEU Chi-restraints excluded: chain D residue 794 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 54 optimal weight: 0.1980 chunk 35 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 HIS ** D 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16360 Z= 0.149 Angle : 0.452 10.106 22392 Z= 0.249 Chirality : 0.039 0.144 2503 Planarity : 0.003 0.035 2710 Dihedral : 15.972 142.575 2744 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.58 % Allowed : 8.52 % Favored : 90.90 % 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: 0.97 (0.20), residues: 1824 helix: 2.76 (0.18), residues: 824 sheet: 0.02 (0.37), residues: 185 loop : -1.56 (0.20), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 629 HIS 0.002 0.001 HIS B 679 PHE 0.006 0.001 PHE B 719 TYR 0.009 0.001 TYR C 266 ARG 0.001 0.000 ARG D 599 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 134 time to evaluate : 2.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 552 MET cc_start: 0.8357 (tpt) cc_final: 0.7751 (tpt) REVERT: D 728 LYS cc_start: 0.7291 (tttm) cc_final: 0.7027 (tttp) REVERT: D 732 ARG cc_start: 0.7208 (ttm-80) cc_final: 0.6997 (mtm110) outliers start: 9 outliers final: 7 residues processed: 141 average time/residue: 0.6946 time to fit residues: 142.9600 Evaluate side-chains 141 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 134 time to evaluate : 2.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 346 ASN Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 346 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 10.0000 chunk 171 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 chunk 167 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 131 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 158 optimal weight: 0.5980 chunk 166 optimal weight: 7.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS A 471 HIS ** D 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 16360 Z= 0.392 Angle : 0.581 10.622 22392 Z= 0.321 Chirality : 0.044 0.166 2503 Planarity : 0.005 0.037 2710 Dihedral : 16.434 140.570 2744 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.65 % Allowed : 8.39 % Favored : 90.97 % 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: 0.41 (0.20), residues: 1824 helix: 2.25 (0.18), residues: 820 sheet: -0.07 (0.38), residues: 186 loop : -1.83 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 415 HIS 0.005 0.001 HIS A 78 PHE 0.014 0.002 PHE A 368 TYR 0.016 0.002 TYR C 266 ARG 0.008 0.001 ARG C 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 145 time to evaluate : 2.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 552 MET cc_start: 0.8373 (tpt) cc_final: 0.7629 (tpt) REVERT: D 728 LYS cc_start: 0.7390 (tttm) cc_final: 0.7132 (tttp) outliers start: 10 outliers final: 6 residues processed: 154 average time/residue: 0.7429 time to fit residues: 161.9356 Evaluate side-chains 143 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 137 time to evaluate : 2.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 346 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 1.9990 chunk 176 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 HIS ** D 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16360 Z= 0.218 Angle : 0.494 10.157 22392 Z= 0.272 Chirality : 0.040 0.152 2503 Planarity : 0.004 0.034 2710 Dihedral : 16.288 142.739 2744 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.58 % Allowed : 9.16 % Favored : 90.26 % 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: 0.58 (0.20), residues: 1824 helix: 2.42 (0.18), residues: 820 sheet: -0.04 (0.38), residues: 185 loop : -1.77 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 629 HIS 0.003 0.001 HIS C 78 PHE 0.008 0.001 PHE A 368 TYR 0.012 0.001 TYR C 266 ARG 0.002 0.000 ARG C 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 139 time to evaluate : 2.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 552 MET cc_start: 0.8394 (tpt) cc_final: 0.7674 (tpt) REVERT: D 728 LYS cc_start: 0.7324 (tttm) cc_final: 0.7103 (tttp) outliers start: 9 outliers final: 8 residues processed: 147 average time/residue: 0.7080 time to fit residues: 149.9451 Evaluate side-chains 144 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 136 time to evaluate : 2.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 346 ASN Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 346 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 0.7980 chunk 157 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.2980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 HIS ** D 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.153932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.115463 restraints weight = 60431.727| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.21 r_work: 0.3107 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16360 Z= 0.225 Angle : 0.498 10.232 22392 Z= 0.273 Chirality : 0.040 0.155 2503 Planarity : 0.004 0.035 2710 Dihedral : 16.303 141.292 2744 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.45 % Allowed : 9.42 % Favored : 90.13 % 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: 0.57 (0.20), residues: 1824 helix: 2.41 (0.18), residues: 822 sheet: -0.04 (0.38), residues: 185 loop : -1.78 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 629 HIS 0.003 0.001 HIS A 78 PHE 0.008 0.001 PHE A 368 TYR 0.012 0.001 TYR C 266 ARG 0.003 0.000 ARG C 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6398.51 seconds wall clock time: 114 minutes 11.81 seconds (6851.81 seconds total)