Starting phenix.real_space_refine on Fri Feb 16 14:06:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rku_4910/02_2024/6rku_4910_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rku_4910/02_2024/6rku_4910.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rku_4910/02_2024/6rku_4910_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rku_4910/02_2024/6rku_4910_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rku_4910/02_2024/6rku_4910_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rku_4910/02_2024/6rku_4910.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rku_4910/02_2024/6rku_4910.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rku_4910/02_2024/6rku_4910_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rku_4910/02_2024/6rku_4910_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians P 64 5.49 5 S 54 5.16 5 C 9570 2.51 5 N 2762 2.21 5 O 3076 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 46": "NH1" <-> "NH2" Residue "A ARG 99": "NH1" <-> "NH2" Residue "A ARG 121": "NH1" <-> "NH2" Residue "A ARG 226": "NH1" <-> "NH2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A ARG 433": "NH1" <-> "NH2" Residue "A ARG 490": "NH1" <-> "NH2" Residue "A ARG 517": "NH1" <-> "NH2" Residue "B ARG 438": "NH1" <-> "NH2" Residue "B ARG 489": "NH1" <-> "NH2" Residue "B ARG 516": "NH1" <-> "NH2" Residue "B ARG 667": "NH1" <-> "NH2" Residue "B ARG 689": "NH1" <-> "NH2" Residue "C ARG 46": "NH1" <-> "NH2" Residue "C ARG 99": "NH1" <-> "NH2" Residue "C ARG 121": "NH1" <-> "NH2" Residue "C ARG 226": "NH1" <-> "NH2" Residue "C ARG 243": "NH1" <-> "NH2" Residue "C ARG 356": "NH1" <-> "NH2" Residue "C ARG 433": "NH1" <-> "NH2" Residue "C ARG 490": "NH1" <-> "NH2" Residue "C ARG 517": "NH1" <-> "NH2" Residue "D ARG 438": "NH1" <-> "NH2" Residue "D ARG 489": "NH1" <-> "NH2" Residue "D ARG 516": "NH1" <-> "NH2" Residue "D ARG 667": "NH1" <-> "NH2" Residue "D ARG 689": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15526 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4022 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 21, 'TRANS': 489} Chain breaks: 2 Chain: "B" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3052 Classifications: {'peptide': 381} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 363} Chain breaks: 1 Chain: "C" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4022 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 21, 'TRANS': 489} Chain breaks: 2 Chain: "D" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3052 Classifications: {'peptide': 381} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 363} Chain breaks: 1 Chain: "F" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 288 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "E" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 288 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "G" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 368 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "H" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 368 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "G" Number of atoms: 66 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 33 Unusual residues: {'JHN': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 33 Unusual residues: {'JHN': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1 AJHN G 101 " occ=0.50 ... (64 atoms not shown) pdb=" O3 BJHN G 101 " occ=0.50 Time building chain proxies: 9.05, per 1000 atoms: 0.58 Number of scatterers: 15526 At special positions: 0 Unit cell: (161.04, 132.88, 124.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 54 16.00 P 64 15.00 O 3076 8.00 N 2762 7.00 C 9570 6.00 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=0, symmetry=0 Time building additional restraints: 6.81 Conformation dependent library (CDL) restraints added in 2.9 seconds 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3340 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 70 helices and 16 sheets defined 43.9% alpha, 10.0% beta 32 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 6.49 Creating SS restraints... Processing helix chain 'A' and resid 14 through 31 removed outlier: 3.594A pdb=" N SER A 20 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR A 21 " --> pdb=" O LYS A 18 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A 22 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE A 29 " --> pdb=" O MET A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 55 Processing helix chain 'A' and resid 66 through 76 Processing helix chain 'A' and resid 83 through 93 removed outlier: 3.509A pdb=" N ALA A 93 " --> pdb=" O ILE A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'A' and resid 131 through 134 No H-bonds generated for 'chain 'A' and resid 131 through 134' Processing helix chain 'A' and resid 165 through 168 No H-bonds generated for 'chain 'A' and resid 165 through 168' Processing helix chain 'A' and resid 187 through 199 Processing helix chain 'A' and resid 205 through 211 Processing helix chain 'A' and resid 226 through 234 Processing helix chain 'A' and resid 270 through 283 Processing helix chain 'A' and resid 314 through 323 Processing helix chain 'A' and resid 347 through 388 removed outlier: 3.658A pdb=" N ALA A 382 " --> pdb=" O HIS A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 399 Processing helix chain 'A' and resid 403 through 412 Processing helix chain 'A' and resid 419 through 421 No H-bonds generated for 'chain 'A' and resid 419 through 421' Processing helix chain 'A' and resid 452 through 459 Processing helix chain 'A' and resid 470 through 493 Processing helix chain 'A' and resid 495 through 513 Processing helix chain 'B' and resid 425 through 435 removed outlier: 3.881A pdb=" N GLY B 430 " --> pdb=" O ASP B 426 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER B 431 " --> pdb=" O SER B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 471 Processing helix chain 'B' and resid 501 through 517 Processing helix chain 'B' and resid 519 through 523 Processing helix chain 'B' and resid 549 through 560 Processing helix chain 'B' and resid 578 through 599 removed outlier: 4.590A pdb=" N ARG B 599 " --> pdb=" O ASN B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 610 removed outlier: 4.289A pdb=" N ILE B 610 " --> pdb=" O LEU B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 620 removed outlier: 3.515A pdb=" N LEU B 620 " --> pdb=" O GLU B 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 617 through 620' Processing helix chain 'B' and resid 623 through 640 Processing helix chain 'B' and resid 679 through 683 Processing helix chain 'B' and resid 685 through 700 removed outlier: 3.943A pdb=" N LEU B 700 " --> pdb=" O LYS B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 731 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 754 Processing helix chain 'B' and resid 773 through 778 removed outlier: 4.498A pdb=" N THR B 778 " --> pdb=" O ASP B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 781 through 786 Processing helix chain 'C' and resid 14 through 31 removed outlier: 3.593A pdb=" N SER C 20 " --> pdb=" O LEU C 17 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR C 21 " --> pdb=" O LYS C 18 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU C 22 " --> pdb=" O SER C 19 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE C 29 " --> pdb=" O MET C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 55 Processing helix chain 'C' and resid 66 through 76 Processing helix chain 'C' and resid 83 through 93 removed outlier: 3.509A pdb=" N ALA C 93 " --> pdb=" O ILE C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 97 No H-bonds generated for 'chain 'C' and resid 95 through 97' Processing helix chain 'C' and resid 131 through 134 No H-bonds generated for 'chain 'C' and resid 131 through 134' Processing helix chain 'C' and resid 165 through 168 No H-bonds generated for 'chain 'C' and resid 165 through 168' Processing helix chain 'C' and resid 187 through 199 Processing helix chain 'C' and resid 205 through 211 Processing helix chain 'C' and resid 226 through 234 Processing helix chain 'C' and resid 270 through 283 Processing helix chain 'C' and resid 314 through 323 Processing helix chain 'C' and resid 347 through 388 removed outlier: 3.657A pdb=" N ALA C 382 " --> pdb=" O HIS C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 399 Processing helix chain 'C' and resid 403 through 412 Processing helix chain 'C' and resid 419 through 421 No H-bonds generated for 'chain 'C' and resid 419 through 421' Processing helix chain 'C' and resid 452 through 459 Processing helix chain 'C' and resid 470 through 493 Processing helix chain 'C' and resid 495 through 513 Processing helix chain 'D' and resid 425 through 435 removed outlier: 3.880A pdb=" N GLY D 430 " --> pdb=" O ASP D 426 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER D 431 " --> pdb=" O SER D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 471 Processing helix chain 'D' and resid 501 through 517 Processing helix chain 'D' and resid 519 through 523 Processing helix chain 'D' and resid 549 through 560 Processing helix chain 'D' and resid 578 through 599 removed outlier: 4.591A pdb=" N ARG D 599 " --> pdb=" O ASN D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 603 through 610 removed outlier: 4.289A pdb=" N ILE D 610 " --> pdb=" O LEU D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 617 through 620 removed outlier: 3.516A pdb=" N LEU D 620 " --> pdb=" O GLU D 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 617 through 620' Processing helix chain 'D' and resid 623 through 640 Processing helix chain 'D' and resid 679 through 683 Processing helix chain 'D' and resid 685 through 700 removed outlier: 3.943A pdb=" N LEU D 700 " --> pdb=" O LYS D 696 " (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 773 through 778 removed outlier: 4.498A pdb=" N THR D 778 " --> pdb=" O ASP D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 781 through 786 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 237 through 243 removed outlier: 3.511A pdb=" N GLY A 238 " --> pdb=" O ILE A 332 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 245 through 250 removed outlier: 3.659A pdb=" N ARG A 245 " --> pdb=" O GLU A 263 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU A 263 " --> pdb=" O ARG A 245 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLU A 247 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N VAL A 261 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLU A 249 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ILE A 259 " --> pdb=" O GLU A 249 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N GLU A 257 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL A 304 " --> pdb=" O ARG A 293 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU A 306 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA A 291 " --> pdb=" O GLU A 306 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 335 through 337 removed outlier: 3.836A pdb=" N ALA A 336 " --> pdb=" O LYS A 343 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 441 through 446 removed outlier: 6.445A pdb=" N GLU B 419 " --> pdb=" O ALA B 442 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N LEU B 444 " --> pdb=" O GLU B 419 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TYR B 421 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LEU B 446 " --> pdb=" O TYR B 421 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL B 423 " --> pdb=" O LEU B 446 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 542 through 546 Processing sheet with id= H, first strand: chain 'B' and resid 646 through 653 removed outlier: 3.517A pdb=" N GLN B 646 " --> pdb=" O ARG B 667 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG B 667 " --> pdb=" O GLN B 646 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS B 652 " --> pdb=" O GLU B 661 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL B 664 " --> pdb=" O TYR B 675 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 103 through 106 Processing sheet with id= J, first strand: chain 'C' and resid 145 through 147 Processing sheet with id= K, first strand: chain 'C' and resid 237 through 243 removed outlier: 3.511A pdb=" N GLY C 238 " --> pdb=" O ILE C 332 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 245 through 250 removed outlier: 3.659A pdb=" N ARG C 245 " --> pdb=" O GLU C 263 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU C 263 " --> pdb=" O ARG C 245 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N GLU C 247 " --> pdb=" O VAL C 261 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N VAL C 261 " --> pdb=" O GLU C 247 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLU C 249 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ILE C 259 " --> pdb=" O GLU C 249 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N GLU C 257 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL C 304 " --> pdb=" O ARG C 293 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU C 306 " --> pdb=" O ALA C 291 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA C 291 " --> pdb=" O GLU C 306 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 335 through 337 removed outlier: 3.836A pdb=" N ALA C 336 " --> pdb=" O LYS C 343 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 441 through 446 removed outlier: 6.445A pdb=" N GLU D 419 " --> pdb=" O ALA D 442 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N LEU D 444 " --> pdb=" O GLU D 419 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N TYR D 421 " --> pdb=" O LEU D 444 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LEU D 446 " --> pdb=" O TYR D 421 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL D 423 " --> pdb=" O LEU D 446 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 542 through 546 Processing sheet with id= P, first strand: chain 'D' and resid 646 through 653 removed outlier: 3.517A pdb=" N GLN D 646 " --> pdb=" O ARG D 667 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG D 667 " --> pdb=" O GLN D 646 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS D 652 " --> pdb=" O GLU D 661 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL D 664 " --> pdb=" O TYR D 675 " (cutoff:3.500A) 568 hydrogen bonds defined for protein. 1608 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 78 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 5.25 Time building geometry restraints manager: 7.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4151 1.33 - 1.45: 2755 1.45 - 1.57: 8792 1.57 - 1.69: 124 1.69 - 1.80: 102 Bond restraints: 15924 Sorted by residual: bond pdb=" C2 BJHN G 101 " pdb=" C3 BJHN G 101 " ideal model delta sigma weight residual 2.160 1.352 0.808 2.00e-02 2.50e+03 1.63e+03 bond pdb=" C2 AJHN G 101 " pdb=" C3 AJHN G 101 " ideal model delta sigma weight residual 2.160 1.352 0.808 2.00e-02 2.50e+03 1.63e+03 bond pdb=" C5 BJHN G 101 " pdb=" C6 BJHN G 101 " ideal model delta sigma weight residual 0.686 1.491 -0.805 2.00e-02 2.50e+03 1.62e+03 bond pdb=" C5 AJHN G 101 " pdb=" C6 AJHN G 101 " ideal model delta sigma weight residual 0.686 1.491 -0.805 2.00e-02 2.50e+03 1.62e+03 bond pdb=" C1 AJHN G 101 " pdb=" C2 AJHN G 101 " ideal model delta sigma weight residual 1.959 1.437 0.522 2.00e-02 2.50e+03 6.81e+02 ... (remaining 15919 not shown) Histogram of bond angle deviations from ideal: 99.89 - 106.71: 799 106.71 - 113.54: 8865 113.54 - 120.36: 5992 120.36 - 127.18: 5906 127.18 - 134.01: 240 Bond angle restraints: 21802 Sorted by residual: angle pdb=" C3 BJHN G 101 " pdb=" C4 BJHN G 101 " pdb=" N1 BJHN G 101 " ideal model delta sigma weight residual 17.58 127.01 -109.43 3.00e+00 1.11e-01 1.33e+03 angle pdb=" C3 AJHN G 101 " pdb=" C4 AJHN G 101 " pdb=" N1 AJHN G 101 " ideal model delta sigma weight residual 17.58 126.93 -109.35 3.00e+00 1.11e-01 1.33e+03 angle pdb=" C1 AJHN G 101 " pdb=" N6 AJHN G 101 " pdb=" C23AJHN G 101 " ideal model delta sigma weight residual 29.62 126.11 -96.49 3.00e+00 1.11e-01 1.03e+03 angle pdb=" C1 BJHN G 101 " pdb=" N6 BJHN G 101 " pdb=" C23BJHN G 101 " ideal model delta sigma weight residual 29.62 125.91 -96.29 3.00e+00 1.11e-01 1.03e+03 angle pdb=" C4 AJHN G 101 " pdb=" C24AJHN G 101 " pdb=" N2 AJHN G 101 " ideal model delta sigma weight residual 65.03 129.23 -64.20 3.00e+00 1.11e-01 4.58e+02 ... (remaining 21797 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.67: 9319 33.67 - 67.33: 243 67.33 - 100.99: 4 100.99 - 134.66: 14 134.66 - 168.32: 6 Dihedral angle restraints: 9586 sinusoidal: 4410 harmonic: 5176 Sorted by residual: dihedral pdb=" C10BJHN G 101 " pdb=" C11BJHN G 101 " pdb=" N4 BJHN G 101 " pdb=" C14BJHN G 101 " ideal model delta sinusoidal sigma weight residual 113.22 -55.10 168.32 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C10AJHN G 101 " pdb=" C11AJHN G 101 " pdb=" N4 AJHN G 101 " pdb=" C14AJHN G 101 " ideal model delta sinusoidal sigma weight residual 113.22 -55.05 168.27 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" CA GLU B 424 " pdb=" C GLU B 424 " pdb=" N GLY B 425 " pdb=" CA GLY B 425 " ideal model delta harmonic sigma weight residual 180.00 -160.00 -20.00 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 9583 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.993: 2446 0.993 - 1.986: 0 1.986 - 2.979: 0 2.979 - 3.972: 0 3.972 - 4.965: 2 Chirality restraints: 2448 Sorted by residual: chirality pdb=" C11BJHN G 101 " pdb=" C10BJHN G 101 " pdb=" C12BJHN G 101 " pdb=" N4 BJHN G 101 " both_signs ideal model delta sigma weight residual False -2.58 2.38 -4.97 2.00e-01 2.50e+01 6.16e+02 chirality pdb=" C11AJHN G 101 " pdb=" C10AJHN G 101 " pdb=" C12AJHN G 101 " pdb=" N4 AJHN G 101 " both_signs ideal model delta sigma weight residual False -2.58 2.35 -4.94 2.00e-01 2.50e+01 6.09e+02 chirality pdb=" C7 AJHN G 101 " pdb=" C23AJHN G 101 " pdb=" C8 AJHN G 101 " pdb=" N2 AJHN G 101 " both_signs ideal model delta sigma weight residual False -2.39 -2.77 0.38 2.00e-01 2.50e+01 3.63e+00 ... (remaining 2445 not shown) Planarity restraints: 2614 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BJHN G 101 " 0.052 2.00e-02 2.50e+03 8.16e-02 2.33e+02 pdb=" C2 BJHN G 101 " 0.009 2.00e-02 2.50e+03 pdb=" C23BJHN G 101 " -0.256 2.00e-02 2.50e+03 pdb=" C24BJHN G 101 " 0.019 2.00e-02 2.50e+03 pdb=" C3 BJHN G 101 " -0.028 2.00e-02 2.50e+03 pdb=" C4 BJHN G 101 " -0.026 2.00e-02 2.50e+03 pdb=" C5 BJHN G 101 " -0.029 2.00e-02 2.50e+03 pdb=" C6 BJHN G 101 " 0.027 2.00e-02 2.50e+03 pdb=" C7 BJHN G 101 " 0.039 2.00e-02 2.50e+03 pdb=" N1 BJHN G 101 " -0.057 2.00e-02 2.50e+03 pdb=" N2 BJHN G 101 " 0.038 2.00e-02 2.50e+03 pdb=" N6 BJHN G 101 " 0.059 2.00e-02 2.50e+03 pdb=" O1 BJHN G 101 " 0.080 2.00e-02 2.50e+03 pdb=" O2 BJHN G 101 " 0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 AJHN G 101 " -0.042 2.00e-02 2.50e+03 6.64e-02 1.54e+02 pdb=" C2 AJHN G 101 " -0.005 2.00e-02 2.50e+03 pdb=" C23AJHN G 101 " 0.205 2.00e-02 2.50e+03 pdb=" C24AJHN G 101 " -0.009 2.00e-02 2.50e+03 pdb=" C3 AJHN G 101 " 0.027 2.00e-02 2.50e+03 pdb=" C4 AJHN G 101 " 0.024 2.00e-02 2.50e+03 pdb=" C5 AJHN G 101 " 0.018 2.00e-02 2.50e+03 pdb=" C6 AJHN G 101 " -0.023 2.00e-02 2.50e+03 pdb=" C7 AJHN G 101 " -0.024 2.00e-02 2.50e+03 pdb=" N1 AJHN G 101 " 0.043 2.00e-02 2.50e+03 pdb=" N2 AJHN G 101 " -0.026 2.00e-02 2.50e+03 pdb=" N6 AJHN G 101 " -0.043 2.00e-02 2.50e+03 pdb=" O1 AJHN G 101 " -0.079 2.00e-02 2.50e+03 pdb=" O2 AJHN G 101 " -0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 780 " -0.016 2.00e-02 2.50e+03 3.28e-02 1.08e+01 pdb=" C LEU B 780 " 0.057 2.00e-02 2.50e+03 pdb=" O LEU B 780 " -0.021 2.00e-02 2.50e+03 pdb=" N MET B 781 " -0.019 2.00e-02 2.50e+03 ... (remaining 2611 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1997 2.75 - 3.29: 14604 3.29 - 3.83: 24155 3.83 - 4.36: 26591 4.36 - 4.90: 45291 Nonbonded interactions: 112638 Sorted by model distance: nonbonded pdb=" O LYS D 538 " pdb=" OG SER D 735 " model vdw 2.215 2.440 nonbonded pdb=" O LYS B 538 " pdb=" OG SER B 735 " model vdw 2.215 2.440 nonbonded pdb=" OE2 GLU B 454 " pdb=" NH1 ARG B 516 " model vdw 2.260 2.520 nonbonded pdb=" OE2 GLU D 454 " pdb=" NH1 ARG D 516 " model vdw 2.260 2.520 nonbonded pdb=" O HIS B 491 " pdb=" ND1 HIS B 526 " model vdw 2.315 2.520 ... (remaining 112633 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' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'G' and resid 15 through 32) selection = chain 'H' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.990 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: 0.010 Extract box with map and model: 10.190 Check model and map are aligned: 0.250 Set scattering table: 0.170 Process input model: 47.230 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 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 : 0.018 0.808 15924 Z= 0.913 Angle : 1.762 109.433 21802 Z= 0.651 Chirality : 0.147 4.965 2448 Planarity : 0.005 0.082 2614 Dihedral : 14.338 168.324 6246 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -2.01 (0.19), residues: 1764 helix: 0.51 (0.17), residues: 818 sheet: -2.18 (0.33), residues: 232 loop : -3.34 (0.19), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 415 HIS 0.005 0.001 HIS C 339 PHE 0.017 0.001 PHE B 514 TYR 0.015 0.001 TYR A 266 ARG 0.006 0.000 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 334 time to evaluate : 1.816 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: A 87 ASP cc_start: 0.8659 (m-30) cc_final: 0.8434 (m-30) REVERT: A 163 ILE cc_start: 0.9189 (mp) cc_final: 0.8975 (pt) REVERT: B 407 LEU cc_start: 0.9279 (tp) cc_final: 0.9037 (tt) REVERT: B 552 MET cc_start: 0.9297 (tpt) cc_final: 0.9014 (tmm) REVERT: B 650 ASP cc_start: 0.8588 (t70) cc_final: 0.6751 (t0) REVERT: B 706 PHE cc_start: 0.6158 (m-80) cc_final: 0.5929 (m-80) REVERT: C 87 ASP cc_start: 0.8736 (m-30) cc_final: 0.8493 (m-30) REVERT: C 298 LYS cc_start: 0.8865 (pttm) cc_final: 0.8600 (mttt) REVERT: C 477 GLU cc_start: 0.8631 (tt0) cc_final: 0.8409 (tt0) REVERT: D 552 MET cc_start: 0.9211 (tpt) cc_final: 0.8956 (tmm) REVERT: D 567 HIS cc_start: 0.7639 (m90) cc_final: 0.6986 (t-90) REVERT: D 706 PHE cc_start: 0.6457 (m-80) cc_final: 0.6065 (m-80) REVERT: D 707 ILE cc_start: 0.8766 (tt) cc_final: 0.8431 (tt) REVERT: D 731 ARG cc_start: 0.8631 (mtt180) cc_final: 0.8380 (mmt90) outliers start: 0 outliers final: 0 residues processed: 334 average time/residue: 0.3446 time to fit residues: 157.7854 Evaluate side-chains 137 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 93 optimal weight: 0.0010 chunk 73 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 165 optimal weight: 4.9990 overall best weight: 1.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 319 ASN A 357 HIS A 378 HIS B 652 HIS C 224 ASN C 319 ASN C 339 HIS C 357 HIS C 378 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.187 15924 Z= 0.289 Angle : 1.411 84.482 21802 Z= 0.530 Chirality : 0.040 0.166 2448 Planarity : 0.005 0.047 2614 Dihedral : 17.111 139.159 2702 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 1.46 % Allowed : 8.62 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -1.16 (0.20), residues: 1764 helix: 1.40 (0.19), residues: 818 sheet: -1.74 (0.36), residues: 218 loop : -3.17 (0.19), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 415 HIS 0.012 0.001 HIS B 652 PHE 0.014 0.001 PHE B 513 TYR 0.014 0.001 TYR A 266 ARG 0.008 0.000 ARG C 272 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 146 time to evaluate : 2.018 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: A 87 ASP cc_start: 0.8659 (m-30) cc_final: 0.8390 (m-30) REVERT: A 124 GLU cc_start: 0.7811 (mp0) cc_final: 0.7552 (pm20) REVERT: A 137 ASP cc_start: 0.7396 (t0) cc_final: 0.7101 (t0) REVERT: A 163 ILE cc_start: 0.9201 (mp) cc_final: 0.8979 (pt) REVERT: B 496 MET cc_start: 0.7887 (mtm) cc_final: 0.7151 (mtt) REVERT: B 552 MET cc_start: 0.9374 (tpt) cc_final: 0.9002 (tmm) REVERT: B 650 ASP cc_start: 0.7693 (t70) cc_final: 0.7074 (t70) REVERT: B 652 HIS cc_start: 0.6150 (m90) cc_final: 0.5877 (m170) REVERT: C 87 ASP cc_start: 0.8735 (m-30) cc_final: 0.8438 (m-30) REVERT: C 124 GLU cc_start: 0.7919 (mp0) cc_final: 0.7571 (pm20) REVERT: C 137 ASP cc_start: 0.7435 (t0) cc_final: 0.7131 (t0) REVERT: C 298 LYS cc_start: 0.8820 (pttm) cc_final: 0.8582 (mttt) REVERT: D 552 MET cc_start: 0.9321 (tpt) cc_final: 0.8946 (tmm) REVERT: D 567 HIS cc_start: 0.7823 (m90) cc_final: 0.7337 (t-170) REVERT: D 616 THR cc_start: 0.7153 (m) cc_final: 0.6918 (p) REVERT: D 706 PHE cc_start: 0.6704 (m-80) cc_final: 0.6325 (m-10) REVERT: D 745 MET cc_start: 0.8440 (ptm) cc_final: 0.8217 (ptm) REVERT: D 755 MET cc_start: 0.9144 (mtm) cc_final: 0.8599 (mtt) outliers start: 22 outliers final: 13 residues processed: 162 average time/residue: 0.3111 time to fit residues: 72.9781 Evaluate side-chains 130 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 117 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain B residue 679 HIS Chi-restraints excluded: chain B residue 718 SER Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 654 ASN Chi-restraints excluded: chain D residue 679 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 137 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 165 optimal weight: 7.9990 chunk 178 optimal weight: 5.9990 chunk 147 optimal weight: 0.0970 chunk 164 optimal weight: 5.9990 chunk 56 optimal weight: 0.0040 chunk 132 optimal weight: 4.9990 overall best weight: 1.2194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.193 15924 Z= 0.285 Angle : 1.383 82.325 21802 Z= 0.515 Chirality : 0.040 0.156 2448 Planarity : 0.005 0.051 2614 Dihedral : 16.987 138.531 2702 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 2.59 % Allowed : 10.08 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -0.68 (0.20), residues: 1764 helix: 1.84 (0.19), residues: 814 sheet: -1.49 (0.36), residues: 218 loop : -2.95 (0.19), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 415 HIS 0.003 0.001 HIS C 338 PHE 0.010 0.001 PHE D 777 TYR 0.012 0.001 TYR A 266 ARG 0.005 0.000 ARG B 731 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 121 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ASP cc_start: 0.8628 (m-30) cc_final: 0.8382 (m-30) REVERT: A 124 GLU cc_start: 0.7985 (mp0) cc_final: 0.7651 (pm20) REVERT: A 137 ASP cc_start: 0.7515 (t0) cc_final: 0.7167 (t0) REVERT: A 163 ILE cc_start: 0.9198 (mp) cc_final: 0.8979 (pt) REVERT: A 505 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8234 (tm-30) REVERT: B 470 LEU cc_start: 0.9389 (mm) cc_final: 0.9159 (mp) REVERT: B 496 MET cc_start: 0.7974 (mtm) cc_final: 0.7224 (mtm) REVERT: B 650 ASP cc_start: 0.7949 (t70) cc_final: 0.7107 (t0) REVERT: B 652 HIS cc_start: 0.6800 (OUTLIER) cc_final: 0.6490 (m170) REVERT: B 745 MET cc_start: 0.8125 (ptm) cc_final: 0.7727 (ppp) REVERT: C 87 ASP cc_start: 0.8675 (m-30) cc_final: 0.8411 (m-30) REVERT: C 124 GLU cc_start: 0.8034 (mp0) cc_final: 0.7669 (pm20) REVERT: C 137 ASP cc_start: 0.7414 (t0) cc_final: 0.7050 (t0) REVERT: C 298 LYS cc_start: 0.8833 (pttm) cc_final: 0.8581 (mttt) REVERT: D 496 MET cc_start: 0.8036 (mtm) cc_final: 0.7563 (mtm) REVERT: D 552 MET cc_start: 0.9328 (tpt) cc_final: 0.8912 (tmm) REVERT: D 567 HIS cc_start: 0.7839 (m90) cc_final: 0.7194 (t-170) REVERT: D 593 MET cc_start: 0.9417 (tmm) cc_final: 0.9193 (tmm) REVERT: D 616 THR cc_start: 0.7220 (m) cc_final: 0.7000 (p) REVERT: D 706 PHE cc_start: 0.6668 (m-80) cc_final: 0.6242 (m-10) outliers start: 39 outliers final: 24 residues processed: 149 average time/residue: 0.2553 time to fit residues: 58.5075 Evaluate side-chains 138 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 113 time to evaluate : 1.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 679 HIS Chi-restraints excluded: chain B residue 718 SER Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 484 ASN Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 671 VAL Chi-restraints excluded: chain D residue 679 HIS Chi-restraints excluded: chain D residue 778 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 0.0470 chunk 124 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 166 optimal weight: 8.9990 chunk 175 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.3682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.192 15924 Z= 0.291 Angle : 1.383 82.284 21802 Z= 0.514 Chirality : 0.039 0.152 2448 Planarity : 0.004 0.051 2614 Dihedral : 16.873 139.068 2702 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 2.32 % Allowed : 10.81 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -0.52 (0.20), residues: 1764 helix: 1.92 (0.19), residues: 828 sheet: -1.42 (0.38), residues: 198 loop : -2.87 (0.19), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 415 HIS 0.003 0.001 HIS A 45 PHE 0.008 0.001 PHE B 777 TYR 0.012 0.001 TYR A 266 ARG 0.007 0.000 ARG D 731 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 109 time to evaluate : 1.893 Fit side-chains revert: symmetry clash REVERT: A 87 ASP cc_start: 0.8625 (m-30) cc_final: 0.8331 (m-30) REVERT: A 124 GLU cc_start: 0.8033 (mp0) cc_final: 0.7715 (pm20) REVERT: A 137 ASP cc_start: 0.7578 (t0) cc_final: 0.7196 (t0) REVERT: A 163 ILE cc_start: 0.9192 (mp) cc_final: 0.8976 (pt) REVERT: A 505 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8237 (tm-30) REVERT: B 593 MET cc_start: 0.9565 (tmm) cc_final: 0.9353 (tmm) REVERT: B 650 ASP cc_start: 0.7878 (t70) cc_final: 0.7036 (t0) REVERT: B 652 HIS cc_start: 0.6800 (OUTLIER) cc_final: 0.6492 (m170) REVERT: B 745 MET cc_start: 0.7924 (ptm) cc_final: 0.7636 (ptm) REVERT: B 755 MET cc_start: 0.8673 (mmm) cc_final: 0.8459 (mmm) REVERT: C 87 ASP cc_start: 0.8668 (m-30) cc_final: 0.8397 (m-30) REVERT: C 124 GLU cc_start: 0.8094 (mp0) cc_final: 0.7741 (pm20) REVERT: C 137 ASP cc_start: 0.7587 (t0) cc_final: 0.7197 (t0) REVERT: C 298 LYS cc_start: 0.8857 (pttm) cc_final: 0.8589 (mttt) REVERT: D 470 LEU cc_start: 0.9018 (mp) cc_final: 0.8283 (mp) REVERT: D 567 HIS cc_start: 0.7820 (m90) cc_final: 0.7151 (t-170) REVERT: D 616 THR cc_start: 0.7333 (m) cc_final: 0.7106 (p) REVERT: D 706 PHE cc_start: 0.6651 (m-80) cc_final: 0.6166 (m-10) outliers start: 35 outliers final: 24 residues processed: 135 average time/residue: 0.2653 time to fit residues: 55.9724 Evaluate side-chains 130 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 105 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain B residue 465 GLN Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 679 HIS Chi-restraints excluded: chain B residue 718 SER Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 759 SER Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 484 ASN Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 679 HIS Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 778 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 72 optimal weight: 8.9990 chunk 150 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 157 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS C 45 HIS ** D 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.198 15924 Z= 0.401 Angle : 1.427 82.160 21802 Z= 0.547 Chirality : 0.042 0.176 2448 Planarity : 0.005 0.056 2614 Dihedral : 16.946 139.783 2702 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 3.12 % Allowed : 10.21 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -0.81 (0.20), residues: 1764 helix: 1.63 (0.19), residues: 824 sheet: -1.61 (0.37), residues: 202 loop : -2.91 (0.18), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 415 HIS 0.004 0.001 HIS A 45 PHE 0.013 0.002 PHE D 777 TYR 0.017 0.002 TYR A 266 ARG 0.007 0.001 ARG C 121 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 106 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ASP cc_start: 0.8671 (m-30) cc_final: 0.8372 (m-30) REVERT: A 124 GLU cc_start: 0.8138 (mp0) cc_final: 0.7815 (pm20) REVERT: A 137 ASP cc_start: 0.7887 (t0) cc_final: 0.7609 (t0) REVERT: A 163 ILE cc_start: 0.9144 (mp) cc_final: 0.8892 (pt) REVERT: A 505 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8251 (tm-30) REVERT: B 550 GLU cc_start: 0.9193 (tt0) cc_final: 0.8982 (pm20) REVERT: B 650 ASP cc_start: 0.7806 (t70) cc_final: 0.7010 (t0) REVERT: B 652 HIS cc_start: 0.6794 (m90) cc_final: 0.6508 (m170) REVERT: B 762 MET cc_start: 0.8349 (ttm) cc_final: 0.8111 (ttm) REVERT: C 87 ASP cc_start: 0.8706 (m-30) cc_final: 0.8423 (m-30) REVERT: C 124 GLU cc_start: 0.8132 (mp0) cc_final: 0.7781 (pm20) REVERT: C 137 ASP cc_start: 0.7851 (t0) cc_final: 0.7547 (t0) REVERT: D 552 MET cc_start: 0.9048 (tpp) cc_final: 0.8697 (tmm) REVERT: D 567 HIS cc_start: 0.7775 (m90) cc_final: 0.7185 (t-170) REVERT: D 706 PHE cc_start: 0.6381 (m-80) cc_final: 0.5958 (m-10) REVERT: D 755 MET cc_start: 0.9004 (mmm) cc_final: 0.8759 (mmm) outliers start: 47 outliers final: 32 residues processed: 144 average time/residue: 0.2372 time to fit residues: 53.8559 Evaluate side-chains 134 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 102 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 679 HIS Chi-restraints excluded: chain B residue 718 SER Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 759 SER Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 484 ASN Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 497 THR Chi-restraints excluded: chain D residue 654 ASN Chi-restraints excluded: chain D residue 679 HIS Chi-restraints excluded: chain D residue 778 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 43 optimal weight: 0.0970 chunk 176 optimal weight: 4.9990 chunk 146 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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: 0.8548 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.193 15924 Z= 0.290 Angle : 1.392 82.359 21802 Z= 0.520 Chirality : 0.040 0.168 2448 Planarity : 0.004 0.051 2614 Dihedral : 16.922 138.929 2702 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 2.52 % Allowed : 11.74 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -0.48 (0.20), residues: 1764 helix: 1.87 (0.19), residues: 828 sheet: -1.20 (0.41), residues: 182 loop : -2.77 (0.18), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 415 HIS 0.002 0.001 HIS A 471 PHE 0.008 0.001 PHE D 777 TYR 0.013 0.001 TYR C 266 ARG 0.005 0.000 ARG D 731 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 108 time to evaluate : 1.786 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ASP cc_start: 0.8651 (m-30) cc_final: 0.8386 (m-30) REVERT: A 124 GLU cc_start: 0.8130 (mp0) cc_final: 0.7813 (pm20) REVERT: A 137 ASP cc_start: 0.7851 (t0) cc_final: 0.7511 (t0) REVERT: A 163 ILE cc_start: 0.9144 (mp) cc_final: 0.8920 (pt) REVERT: A 505 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8265 (tm-30) REVERT: B 550 GLU cc_start: 0.9146 (tt0) cc_final: 0.8901 (pm20) REVERT: B 650 ASP cc_start: 0.7826 (t70) cc_final: 0.6983 (t0) REVERT: B 652 HIS cc_start: 0.6812 (OUTLIER) cc_final: 0.6519 (m170) REVERT: B 745 MET cc_start: 0.8051 (ptm) cc_final: 0.7790 (ptm) REVERT: C 87 ASP cc_start: 0.8691 (m-30) cc_final: 0.8389 (m-30) REVERT: C 124 GLU cc_start: 0.8135 (mp0) cc_final: 0.7828 (pm20) REVERT: C 137 ASP cc_start: 0.7826 (t0) cc_final: 0.7483 (t0) REVERT: D 552 MET cc_start: 0.9031 (tpp) cc_final: 0.8669 (tmm) REVERT: D 567 HIS cc_start: 0.7708 (m90) cc_final: 0.6887 (t70) REVERT: D 731 ARG cc_start: 0.7156 (mmt90) cc_final: 0.6637 (mmt180) REVERT: D 745 MET cc_start: 0.7636 (ptm) cc_final: 0.7142 (ppp) REVERT: D 755 MET cc_start: 0.8918 (mmm) cc_final: 0.8685 (mmm) outliers start: 38 outliers final: 30 residues processed: 140 average time/residue: 0.2433 time to fit residues: 53.9890 Evaluate side-chains 136 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 105 time to evaluate : 1.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 679 HIS Chi-restraints excluded: chain B residue 718 SER Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 484 ASN Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 497 THR Chi-restraints excluded: chain D residue 654 ASN Chi-restraints excluded: chain D residue 679 HIS Chi-restraints excluded: chain D residue 778 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 128 optimal weight: 0.7980 chunk 99 optimal weight: 0.6980 chunk 148 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 175 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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: 0.8526 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.192 15924 Z= 0.273 Angle : 1.385 82.323 21802 Z= 0.514 Chirality : 0.039 0.138 2448 Planarity : 0.004 0.051 2614 Dihedral : 16.892 140.542 2702 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 2.45 % Allowed : 12.14 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -0.27 (0.21), residues: 1764 helix: 2.03 (0.19), residues: 828 sheet: -0.98 (0.42), residues: 182 loop : -2.69 (0.18), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 415 HIS 0.002 0.000 HIS A 471 PHE 0.011 0.001 PHE B 706 TYR 0.011 0.001 TYR C 266 ARG 0.005 0.000 ARG D 731 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 110 time to evaluate : 1.854 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ASP cc_start: 0.8606 (m-30) cc_final: 0.8314 (m-30) REVERT: A 124 GLU cc_start: 0.8124 (mp0) cc_final: 0.7811 (pm20) REVERT: A 137 ASP cc_start: 0.7827 (t0) cc_final: 0.7449 (t0) REVERT: A 505 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8258 (tm-30) REVERT: B 650 ASP cc_start: 0.7875 (t70) cc_final: 0.7056 (t0) REVERT: B 652 HIS cc_start: 0.6787 (OUTLIER) cc_final: 0.6485 (m170) REVERT: C 87 ASP cc_start: 0.8676 (m-30) cc_final: 0.8407 (m-30) REVERT: C 124 GLU cc_start: 0.8114 (mp0) cc_final: 0.7803 (pm20) REVERT: C 137 ASP cc_start: 0.7848 (t0) cc_final: 0.7475 (t0) REVERT: D 552 MET cc_start: 0.9048 (tpp) cc_final: 0.8689 (tmm) REVERT: D 567 HIS cc_start: 0.7692 (m90) cc_final: 0.6894 (t70) REVERT: D 706 PHE cc_start: 0.6362 (m-80) cc_final: 0.5860 (m-80) REVERT: D 731 ARG cc_start: 0.7226 (mmt90) cc_final: 0.6739 (mmt180) outliers start: 37 outliers final: 31 residues processed: 143 average time/residue: 0.2529 time to fit residues: 57.4243 Evaluate side-chains 136 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 104 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 679 HIS Chi-restraints excluded: chain B residue 718 SER Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 484 ASN Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 497 THR Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 679 HIS Chi-restraints excluded: chain D residue 778 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 2.9990 chunk 70 optimal weight: 0.1980 chunk 104 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 119 optimal weight: 0.7980 chunk 86 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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: 0.8513 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.191 15924 Z= 0.272 Angle : 1.385 82.309 21802 Z= 0.513 Chirality : 0.039 0.151 2448 Planarity : 0.004 0.050 2614 Dihedral : 16.795 141.755 2702 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.72 % Allowed : 12.33 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -0.08 (0.21), residues: 1764 helix: 2.16 (0.19), residues: 814 sheet: -0.78 (0.43), residues: 182 loop : -2.48 (0.19), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 415 HIS 0.002 0.000 HIS A 45 PHE 0.007 0.001 PHE B 777 TYR 0.010 0.001 TYR C 266 ARG 0.003 0.000 ARG D 731 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 106 time to evaluate : 1.793 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ASP cc_start: 0.8590 (m-30) cc_final: 0.8317 (m-30) REVERT: A 92 MET cc_start: 0.9005 (OUTLIER) cc_final: 0.8256 (mtm) REVERT: A 124 GLU cc_start: 0.8105 (mp0) cc_final: 0.7805 (pm20) REVERT: A 137 ASP cc_start: 0.7724 (t0) cc_final: 0.7314 (t0) REVERT: A 505 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8260 (tm-30) REVERT: B 650 ASP cc_start: 0.7831 (t70) cc_final: 0.6978 (t0) REVERT: B 652 HIS cc_start: 0.6892 (OUTLIER) cc_final: 0.6615 (m170) REVERT: B 731 ARG cc_start: 0.7489 (mmt180) cc_final: 0.7268 (mpt180) REVERT: C 87 ASP cc_start: 0.8671 (m-30) cc_final: 0.8398 (m-30) REVERT: C 124 GLU cc_start: 0.8079 (mp0) cc_final: 0.7780 (pm20) REVERT: C 137 ASP cc_start: 0.7793 (t0) cc_final: 0.7406 (t0) REVERT: C 301 MET cc_start: 0.8373 (ppp) cc_final: 0.8100 (ppp) REVERT: D 552 MET cc_start: 0.9066 (tpp) cc_final: 0.8704 (tmm) REVERT: D 567 HIS cc_start: 0.7697 (m90) cc_final: 0.6882 (t70) REVERT: D 706 PHE cc_start: 0.6312 (m-80) cc_final: 0.5773 (m-80) REVERT: D 731 ARG cc_start: 0.7283 (mmt90) cc_final: 0.6795 (mmt180) outliers start: 41 outliers final: 28 residues processed: 142 average time/residue: 0.2461 time to fit residues: 54.5263 Evaluate side-chains 133 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 103 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 679 HIS Chi-restraints excluded: chain B residue 718 SER Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 484 ASN Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 497 THR Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 679 HIS Chi-restraints excluded: chain D residue 778 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 0.9990 chunk 168 optimal weight: 3.9990 chunk 153 optimal weight: 6.9990 chunk 163 optimal weight: 0.0170 chunk 98 optimal weight: 0.9990 chunk 71 optimal weight: 0.0270 chunk 128 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 147 optimal weight: 0.0570 chunk 154 optimal weight: 2.9990 chunk 162 optimal weight: 0.8980 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.189 15924 Z= 0.255 Angle : 1.391 82.304 21802 Z= 0.513 Chirality : 0.039 0.138 2448 Planarity : 0.004 0.049 2614 Dihedral : 16.717 142.472 2702 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.12 % Allowed : 12.93 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: 0.02 (0.21), residues: 1764 helix: 2.22 (0.19), residues: 812 sheet: -0.52 (0.43), residues: 182 loop : -2.46 (0.19), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 415 HIS 0.002 0.000 HIS A 45 PHE 0.015 0.001 PHE B 706 TYR 0.008 0.001 TYR B 421 ARG 0.005 0.000 ARG C 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 112 time to evaluate : 1.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ASP cc_start: 0.8558 (m-30) cc_final: 0.8289 (m-30) REVERT: A 92 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8281 (mtm) REVERT: A 137 ASP cc_start: 0.7587 (t0) cc_final: 0.7136 (t0) REVERT: B 407 LEU cc_start: 0.8898 (tt) cc_final: 0.8652 (mp) REVERT: B 650 ASP cc_start: 0.7808 (t70) cc_final: 0.6950 (t0) REVERT: B 652 HIS cc_start: 0.6936 (OUTLIER) cc_final: 0.6689 (m170) REVERT: B 750 LEU cc_start: 0.9469 (tp) cc_final: 0.9231 (mp) REVERT: C 87 ASP cc_start: 0.8647 (m-30) cc_final: 0.8389 (m-30) REVERT: C 101 MET cc_start: 0.8825 (mmm) cc_final: 0.8482 (mmt) REVERT: C 137 ASP cc_start: 0.7667 (t0) cc_final: 0.7214 (t0) REVERT: C 301 MET cc_start: 0.8264 (ppp) cc_final: 0.8046 (ppp) REVERT: D 567 HIS cc_start: 0.7717 (m90) cc_final: 0.7159 (t70) REVERT: D 706 PHE cc_start: 0.6382 (m-80) cc_final: 0.5913 (m-10) REVERT: D 731 ARG cc_start: 0.7268 (mmt90) cc_final: 0.6787 (mmt180) outliers start: 32 outliers final: 22 residues processed: 136 average time/residue: 0.2583 time to fit residues: 54.5093 Evaluate side-chains 130 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 106 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 679 HIS Chi-restraints excluded: chain B residue 718 SER Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 755 MET Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 484 ASN Chi-restraints excluded: chain D residue 497 THR Chi-restraints excluded: chain D residue 654 ASN Chi-restraints excluded: chain D residue 679 HIS Chi-restraints excluded: chain D residue 778 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 0.9980 chunk 172 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 181 optimal weight: 0.7980 chunk 166 optimal weight: 6.9990 chunk 144 optimal weight: 0.9990 chunk 14 optimal weight: 0.0010 chunk 111 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 531 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.190 15924 Z= 0.263 Angle : 1.393 82.256 21802 Z= 0.514 Chirality : 0.039 0.154 2448 Planarity : 0.004 0.049 2614 Dihedral : 16.679 143.198 2702 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.86 % Allowed : 12.93 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: 0.11 (0.21), residues: 1764 helix: 2.25 (0.19), residues: 810 sheet: -0.43 (0.43), residues: 182 loop : -2.35 (0.19), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 415 HIS 0.002 0.000 HIS C 338 PHE 0.006 0.001 PHE D 513 TYR 0.010 0.001 TYR D 421 ARG 0.003 0.000 ARG D 731 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 109 time to evaluate : 1.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ASP cc_start: 0.8565 (m-30) cc_final: 0.8295 (m-30) REVERT: A 92 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.8197 (mtm) REVERT: A 137 ASP cc_start: 0.7597 (t0) cc_final: 0.7159 (t0) REVERT: B 650 ASP cc_start: 0.7841 (t70) cc_final: 0.6964 (t0) REVERT: B 652 HIS cc_start: 0.6933 (OUTLIER) cc_final: 0.6694 (m170) REVERT: C 87 ASP cc_start: 0.8659 (m-30) cc_final: 0.8397 (m-30) REVERT: C 101 MET cc_start: 0.8889 (mmm) cc_final: 0.8462 (mmt) REVERT: C 137 ASP cc_start: 0.7630 (t0) cc_final: 0.7205 (t0) REVERT: D 567 HIS cc_start: 0.7708 (m90) cc_final: 0.7152 (t70) REVERT: D 706 PHE cc_start: 0.6349 (m-80) cc_final: 0.5860 (m-80) REVERT: D 731 ARG cc_start: 0.7292 (mmt90) cc_final: 0.6818 (mmt180) outliers start: 28 outliers final: 20 residues processed: 134 average time/residue: 0.2793 time to fit residues: 58.2112 Evaluate side-chains 125 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 103 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 679 HIS Chi-restraints excluded: chain B residue 718 SER Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 484 ASN Chi-restraints excluded: chain D residue 497 THR Chi-restraints excluded: chain D residue 679 HIS Chi-restraints excluded: chain D residue 778 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 chunk 44 optimal weight: 0.0570 chunk 133 optimal weight: 0.2980 chunk 21 optimal weight: 0.0060 chunk 40 optimal weight: 4.9990 chunk 144 optimal weight: 0.6980 chunk 60 optimal weight: 0.0870 chunk 148 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.2292 ------------------------------------------------------------------------------- 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 = 0.3338 r_free = 0.3338 target = 0.070453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.055638 restraints weight = 70196.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.057178 restraints weight = 38034.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.058242 restraints weight = 24749.524| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.188 15924 Z= 0.257 Angle : 1.400 82.267 21802 Z= 0.517 Chirality : 0.039 0.161 2448 Planarity : 0.004 0.049 2614 Dihedral : 16.639 143.150 2702 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.46 % Allowed : 13.73 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: 0.11 (0.21), residues: 1764 helix: 2.15 (0.19), residues: 824 sheet: -0.41 (0.42), residues: 186 loop : -2.33 (0.19), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 415 HIS 0.002 0.000 HIS A 45 PHE 0.013 0.001 PHE B 706 TYR 0.009 0.001 TYR D 421 ARG 0.004 0.000 ARG D 731 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2929.36 seconds wall clock time: 54 minutes 14.62 seconds (3254.62 seconds total)