Starting phenix.real_space_refine on Sat Jan 20 06:15:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aib_11794/01_2024/7aib_11794_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aib_11794/01_2024/7aib_11794.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aib_11794/01_2024/7aib_11794.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aib_11794/01_2024/7aib_11794.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aib_11794/01_2024/7aib_11794_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aib_11794/01_2024/7aib_11794_updated.pdb" } resolution = 4.7 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= 0.011 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 66 5.49 5 S 41 5.16 5 C 8493 2.51 5 N 2500 2.21 5 O 2739 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 784": "OE1" <-> "OE2" Residue "B ASP 270": "OD1" <-> "OD2" Residue "B TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 594": "OE1" <-> "OE2" Residue "B PHE 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 784": "OE1" <-> "OE2" Residue "C TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 167": "OE1" <-> "OE2" Residue "C ASP 233": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 13839 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5206 Classifications: {'peptide': 661} Link IDs: {'PTRANS': 27, 'TRANS': 633} Chain breaks: 1 Chain: "B" Number of atoms: 5225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5225 Classifications: {'peptide': 663} Link IDs: {'PTRANS': 27, 'TRANS': 635} Chain breaks: 1 Chain: "C" Number of atoms: 2116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2116 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 9, 'TRANS': 257} Chain breaks: 3 Chain: "D" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 621 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "E" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 609 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.67, per 1000 atoms: 0.55 Number of scatterers: 13839 At special positions: 0 Unit cell: (133.76, 110.88, 130.24, 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 41 16.00 P 66 15.00 O 2739 8.00 N 2500 7.00 C 8493 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: 5.79 Conformation dependent library (CDL) restraints added in 2.4 seconds 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2980 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 62 helices and 12 sheets defined 45.4% alpha, 12.9% beta 30 base pairs and 58 stacking pairs defined. Time for finding SS restraints: 6.80 Creating SS restraints... Processing helix chain 'A' and resid 163 through 173 Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 206 through 217 Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 231 through 247 removed outlier: 4.110A pdb=" N ALA A 236 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS A 246 " --> pdb=" O GLN A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 277 Processing helix chain 'A' and resid 291 through 295 Processing helix chain 'A' and resid 301 through 312 Processing helix chain 'A' and resid 318 through 331 Processing helix chain 'A' and resid 335 through 343 Proline residue: A 340 - end of helix Processing helix chain 'A' and resid 348 through 356 Processing helix chain 'A' and resid 362 through 381 removed outlier: 3.967A pdb=" N GLN A 374 " --> pdb=" O HIS A 370 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 375 " --> pdb=" O ALA A 371 " (cutoff:3.500A) Proline residue: A 376 - end of helix Processing helix chain 'A' and resid 388 through 397 Processing helix chain 'A' and resid 401 through 410 Processing helix chain 'A' and resid 431 through 441 removed outlier: 3.755A pdb=" N ALA A 440 " --> pdb=" O TRP A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 458 Processing helix chain 'A' and resid 479 through 484 removed outlier: 4.579A pdb=" N HIS A 483 " --> pdb=" O ARG A 479 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LEU A 484 " --> pdb=" O GLY A 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 479 through 484' Processing helix chain 'A' and resid 504 through 564 removed outlier: 3.865A pdb=" N PHE A 532 " --> pdb=" O TYR A 528 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP A 533 " --> pdb=" O GLU A 529 " (cutoff:3.500A) Proline residue: A 537 - end of helix removed outlier: 4.744A pdb=" N GLU A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ALA A 541 " --> pdb=" O PRO A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 591 No H-bonds generated for 'chain 'A' and resid 588 through 591' Processing helix chain 'A' and resid 620 through 636 Processing helix chain 'A' and resid 673 through 683 removed outlier: 3.560A pdb=" N ASN A 679 " --> pdb=" O THR A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 717 Processing helix chain 'A' and resid 730 through 734 Processing helix chain 'A' and resid 772 through 779 removed outlier: 3.941A pdb=" N ALA A 777 " --> pdb=" O LEU A 773 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU A 778 " --> pdb=" O ALA A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 796 removed outlier: 3.792A pdb=" N GLU A 795 " --> pdb=" O GLN A 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 173 Processing helix chain 'B' and resid 187 through 189 No H-bonds generated for 'chain 'B' and resid 187 through 189' Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'B' and resid 206 through 217 Processing helix chain 'B' and resid 223 through 225 No H-bonds generated for 'chain 'B' and resid 223 through 225' Processing helix chain 'B' and resid 231 through 247 removed outlier: 4.092A pdb=" N ALA B 236 " --> pdb=" O ARG B 232 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYS B 246 " --> pdb=" O GLN B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 291 through 295 Processing helix chain 'B' and resid 301 through 312 Processing helix chain 'B' and resid 318 through 331 Processing helix chain 'B' and resid 335 through 343 Proline residue: B 340 - end of helix Processing helix chain 'B' and resid 348 through 357 Processing helix chain 'B' and resid 362 through 381 removed outlier: 3.947A pdb=" N GLN B 374 " --> pdb=" O HIS B 370 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU B 375 " --> pdb=" O ALA B 371 " (cutoff:3.500A) Proline residue: B 376 - end of helix Processing helix chain 'B' and resid 388 through 397 Processing helix chain 'B' and resid 401 through 410 Processing helix chain 'B' and resid 431 through 441 removed outlier: 3.732A pdb=" N ALA B 440 " --> pdb=" O TRP B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 458 Processing helix chain 'B' and resid 479 through 484 removed outlier: 4.559A pdb=" N HIS B 483 " --> pdb=" O ARG B 479 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N LEU B 484 " --> pdb=" O GLY B 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 479 through 484' Processing helix chain 'B' and resid 504 through 565 removed outlier: 3.615A pdb=" N ASP B 511 " --> pdb=" O LYS B 507 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 512 " --> pdb=" O GLU B 508 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY B 518 " --> pdb=" O LEU B 514 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE B 532 " --> pdb=" O TYR B 528 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP B 533 " --> pdb=" O GLU B 529 " (cutoff:3.500A) Proline residue: B 537 - end of helix removed outlier: 4.825A pdb=" N GLU B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ALA B 541 " --> pdb=" O PRO B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 591 No H-bonds generated for 'chain 'B' and resid 588 through 591' Processing helix chain 'B' and resid 620 through 636 Processing helix chain 'B' and resid 673 through 683 Processing helix chain 'B' and resid 703 through 717 Processing helix chain 'B' and resid 730 through 734 Processing helix chain 'B' and resid 772 through 779 removed outlier: 3.923A pdb=" N ALA B 777 " --> pdb=" O LEU B 773 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU B 778 " --> pdb=" O ALA B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 796 removed outlier: 3.802A pdb=" N GLU B 795 " --> pdb=" O GLN B 791 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 37 Processing helix chain 'C' and resid 48 through 50 No H-bonds generated for 'chain 'C' and resid 48 through 50' Processing helix chain 'C' and resid 65 through 70 removed outlier: 3.919A pdb=" N ALA C 69 " --> pdb=" O LYS C 65 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU C 70 " --> pdb=" O ASP C 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 65 through 70' Processing helix chain 'C' and resid 96 through 103 Processing helix chain 'C' and resid 156 through 159 No H-bonds generated for 'chain 'C' and resid 156 through 159' Processing helix chain 'C' and resid 166 through 181 Processing helix chain 'C' and resid 209 through 223 removed outlier: 6.792A pdb=" N THR C 218 " --> pdb=" O ALA C 214 " (cutoff:3.500A) removed outlier: 9.120A pdb=" N ALA C 219 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N PHE C 220 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU C 221 " --> pdb=" O GLY C 217 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN C 223 " --> pdb=" O ALA C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 252 No H-bonds generated for 'chain 'C' and resid 250 through 252' Processing helix chain 'C' and resid 266 through 275 Processing helix chain 'C' and resid 316 through 330 removed outlier: 3.781A pdb=" N SER C 328 " --> pdb=" O GLN C 324 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL C 329 " --> pdb=" O GLY C 325 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 196 through 199 removed outlier: 6.495A pdb=" N LEU A 178 " --> pdb=" O ARG A 197 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ARG A 199 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N TYR A 180 " --> pdb=" O ARG A 199 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA A 181 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N GLN A 138 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR A 147 " --> pdb=" O ARG A 156 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG A 156 " --> pdb=" O THR A 147 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 464 through 468 removed outlier: 5.882A pdb=" N ILE A 502 " --> pdb=" O ARG A 491 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ARG A 491 " --> pdb=" O ILE A 502 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 578 through 581 Processing sheet with id= D, first strand: chain 'A' and resid 609 through 614 removed outlier: 3.563A pdb=" N THR A 613 " --> pdb=" O VAL A 745 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU A 747 " --> pdb=" O THR A 613 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 653 through 655 removed outlier: 6.696A pdb=" N LEU A 689 " --> pdb=" O PHE A 654 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU A 722 " --> pdb=" O VAL A 690 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N MET A 692 " --> pdb=" O LEU A 722 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU A 724 " --> pdb=" O MET A 692 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 749 through 752 Processing sheet with id= G, first strand: chain 'B' and resid 196 through 199 removed outlier: 6.495A pdb=" N LEU B 178 " --> pdb=" O ARG B 197 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ARG B 199 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N TYR B 180 " --> pdb=" O ARG B 199 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ALA B 181 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N GLN B 138 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG B 156 " --> pdb=" O THR B 147 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 464 through 468 removed outlier: 5.902A pdb=" N ILE B 502 " --> pdb=" O ARG B 491 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ARG B 491 " --> pdb=" O ILE B 502 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 578 through 581 Processing sheet with id= J, first strand: chain 'B' and resid 755 through 764 removed outlier: 6.820A pdb=" N ASP B 748 " --> pdb=" O MET B 759 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N SER B 761 " --> pdb=" O HIS B 746 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N HIS B 746 " --> pdb=" O SER B 761 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N GLN B 763 " --> pdb=" O ASN B 744 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ASN B 744 " --> pdb=" O GLN B 763 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N MET B 609 " --> pdb=" O ALA B 743 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL B 745 " --> pdb=" O MET B 609 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ILE B 611 " --> pdb=" O VAL B 745 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU B 747 " --> pdb=" O ILE B 611 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N THR B 613 " --> pdb=" O LEU B 747 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N ALA B 749 " --> pdb=" O THR B 613 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N THR B 723 " --> pdb=" O LEU B 610 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ILE B 612 " --> pdb=" O THR B 723 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N PHE B 725 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N GLY B 614 " --> pdb=" O PHE B 725 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 110 through 113 removed outlier: 4.139A pdb=" N THR C 143 " --> pdb=" O ASP C 58 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR C 186 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ILE C 44 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ASN C 188 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ILE C 46 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N SER C 190 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N HIS C 191 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ILE C 195 " --> pdb=" O HIS C 191 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 224 through 231 removed outlier: 3.507A pdb=" N LEU C 290 " --> pdb=" O TYR C 255 " (cutoff:3.500A) 538 hydrogen bonds defined for protein. 1563 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 76 hydrogen bonds 152 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 58 stacking parallelities Total time for adding SS restraints: 5.11 Time building geometry restraints manager: 6.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2240 1.31 - 1.44: 3805 1.44 - 1.57: 7941 1.57 - 1.70: 128 1.70 - 1.83: 80 Bond restraints: 14194 Sorted by residual: bond pdb=" N3B ANP B1801 " pdb=" PG ANP B1801 " ideal model delta sigma weight residual 1.795 1.632 0.163 2.00e-02 2.50e+03 6.63e+01 bond pdb=" N3B ANP A1801 " pdb=" PG ANP A1801 " ideal model delta sigma weight residual 1.795 1.634 0.161 2.00e-02 2.50e+03 6.47e+01 bond pdb=" CE1 HIS A 682 " pdb=" NE2 HIS A 682 " ideal model delta sigma weight residual 1.321 1.373 -0.052 1.00e-02 1.00e+04 2.75e+01 bond pdb=" N ILE A 503 " pdb=" CA ILE A 503 " ideal model delta sigma weight residual 1.462 1.506 -0.044 8.70e-03 1.32e+04 2.57e+01 bond pdb=" O3A ANP B1801 " pdb=" PB ANP B1801 " ideal model delta sigma weight residual 1.700 1.603 0.097 2.00e-02 2.50e+03 2.35e+01 ... (remaining 14189 not shown) Histogram of bond angle deviations from ideal: 96.43 - 104.04: 356 104.04 - 111.64: 5917 111.64 - 119.24: 7250 119.24 - 126.84: 5700 126.84 - 134.45: 257 Bond angle restraints: 19480 Sorted by residual: angle pdb=" C PHE A 143 " pdb=" N GLY A 144 " pdb=" CA GLY A 144 " ideal model delta sigma weight residual 121.65 127.06 -5.41 6.80e-01 2.16e+00 6.32e+01 angle pdb=" N LEU C 150 " pdb=" CA LEU C 150 " pdb=" C LEU C 150 " ideal model delta sigma weight residual 111.07 102.93 8.14 1.07e+00 8.73e-01 5.78e+01 angle pdb=" N ASP A 265 " pdb=" CA ASP A 265 " pdb=" C ASP A 265 " ideal model delta sigma weight residual 111.33 103.23 8.10 1.21e+00 6.83e-01 4.48e+01 angle pdb=" N ILE A 695 " pdb=" CA ILE A 695 " pdb=" C ILE A 695 " ideal model delta sigma weight residual 109.37 100.49 8.88 1.35e+00 5.49e-01 4.32e+01 angle pdb=" C PHE B 143 " pdb=" N GLY B 144 " pdb=" CA GLY B 144 " ideal model delta sigma weight residual 121.65 126.09 -4.44 6.80e-01 2.16e+00 4.26e+01 ... (remaining 19475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.66: 7876 31.66 - 63.31: 603 63.31 - 94.97: 48 94.97 - 126.63: 0 126.63 - 158.28: 2 Dihedral angle restraints: 8529 sinusoidal: 3918 harmonic: 4611 Sorted by residual: dihedral pdb=" N TYR C 152 " pdb=" C TYR C 152 " pdb=" CA TYR C 152 " pdb=" CB TYR C 152 " ideal model delta harmonic sigma weight residual 122.80 134.39 -11.59 0 2.50e+00 1.60e-01 2.15e+01 dihedral pdb=" C THR C 109 " pdb=" N THR C 109 " pdb=" CA THR C 109 " pdb=" CB THR C 109 " ideal model delta harmonic sigma weight residual -122.00 -133.58 11.58 0 2.50e+00 1.60e-01 2.15e+01 dihedral pdb=" C TYR C 152 " pdb=" N TYR C 152 " pdb=" CA TYR C 152 " pdb=" CB TYR C 152 " ideal model delta harmonic sigma weight residual -122.60 -133.98 11.38 0 2.50e+00 1.60e-01 2.07e+01 ... (remaining 8526 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1253 0.082 - 0.164: 806 0.164 - 0.247: 142 0.247 - 0.329: 15 0.329 - 0.411: 2 Chirality restraints: 2218 Sorted by residual: chirality pdb=" CA TYR C 152 " pdb=" N TYR C 152 " pdb=" C TYR C 152 " pdb=" CB TYR C 152 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" C3' ANP A1801 " pdb=" C2' ANP A1801 " pdb=" C4' ANP A1801 " pdb=" O3' ANP A1801 " both_signs ideal model delta sigma weight residual False -2.36 -2.70 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" C3' DG D 31 " pdb=" C4' DG D 31 " pdb=" O3' DG D 31 " pdb=" C2' DG D 31 " both_signs ideal model delta sigma weight residual False -2.66 -2.34 -0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 2215 not shown) Planarity restraints: 2319 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE C 168 " -0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C PHE C 168 " 0.063 2.00e-02 2.50e+03 pdb=" O PHE C 168 " -0.024 2.00e-02 2.50e+03 pdb=" N ASN C 169 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 623 " 0.034 2.00e-02 2.50e+03 2.38e-02 1.13e+01 pdb=" CG TYR A 623 " 0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR A 623 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR A 623 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR A 623 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR A 623 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR A 623 " -0.020 2.00e-02 2.50e+03 pdb=" OH TYR A 623 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 215 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C LEU A 215 " 0.055 2.00e-02 2.50e+03 pdb=" O LEU A 215 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN A 216 " -0.019 2.00e-02 2.50e+03 ... (remaining 2316 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 2474 2.84 - 3.36: 14248 3.36 - 3.87: 23285 3.87 - 4.39: 30238 4.39 - 4.90: 45568 Nonbonded interactions: 115813 Sorted by model distance: nonbonded pdb=" O LEU B 295 " pdb=" ND2 ASN B 557 " model vdw 2.329 2.520 nonbonded pdb=" O PHE B 730 " pdb=" OG1 THR B 733 " model vdw 2.330 2.440 nonbonded pdb=" OG SER C 112 " pdb=" O GLY C 142 " model vdw 2.336 2.440 nonbonded pdb=" O LEU A 295 " pdb=" ND2 ASN A 557 " model vdw 2.351 2.520 nonbonded pdb=" O ARG B 232 " pdb=" OG SER B 235 " model vdw 2.351 2.440 ... (remaining 115808 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 'B' and (resid 128 through 659 or resid 672 through 800 or resid 1801)) } 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 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: 0.370 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: 0.020 Extract box with map and model: 2.270 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 44.750 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 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 : 0.014 0.163 14194 Z= 0.904 Angle : 1.844 12.159 19480 Z= 1.350 Chirality : 0.096 0.411 2218 Planarity : 0.006 0.037 2319 Dihedral : 19.505 158.283 5549 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.14 % Allowed : 6.68 % Favored : 92.19 % Cbeta Deviations : 0.20 % 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: -3.64 (0.17), residues: 1575 helix: -2.22 (0.15), residues: 704 sheet: -2.30 (0.36), residues: 156 loop : -2.55 (0.20), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP A 709 HIS 0.010 0.002 HIS B 254 PHE 0.032 0.006 PHE A 758 TYR 0.044 0.005 TYR A 623 ARG 0.034 0.002 ARG A 790 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 210 time to evaluate : 1.640 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 MET cc_start: 0.8272 (tpt) cc_final: 0.7971 (tpt) REVERT: A 306 MET cc_start: 0.8626 (ttm) cc_final: 0.8143 (ttt) REVERT: A 534 LEU cc_start: 0.9130 (mt) cc_final: 0.8490 (mt) REVERT: A 552 LEU cc_start: 0.9372 (mt) cc_final: 0.9149 (mt) REVERT: A 633 MET cc_start: 0.7882 (mtp) cc_final: 0.7578 (tpp) REVERT: A 674 MET cc_start: 0.8520 (mmp) cc_final: 0.8268 (mpp) REVERT: A 679 ASN cc_start: 0.8367 (t0) cc_final: 0.7775 (m-40) REVERT: A 692 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.7406 (mmm) REVERT: A 750 LEU cc_start: 0.8417 (mt) cc_final: 0.7477 (mm) REVERT: B 213 LEU cc_start: 0.9597 (mt) cc_final: 0.9268 (mm) REVERT: B 222 LEU cc_start: 0.8148 (mt) cc_final: 0.7593 (mt) REVERT: B 260 MET cc_start: 0.8995 (ttt) cc_final: 0.7700 (ttp) REVERT: B 269 MET cc_start: 0.7955 (ttm) cc_final: 0.7084 (ttm) REVERT: B 386 ASP cc_start: 0.7717 (t0) cc_final: 0.7509 (m-30) REVERT: B 609 MET cc_start: 0.8230 (ttm) cc_final: 0.7575 (mtm) REVERT: B 691 LEU cc_start: 0.8748 (mt) cc_final: 0.8420 (mp) REVERT: C 28 LYS cc_start: 0.9574 (tttt) cc_final: 0.9255 (ttmm) REVERT: C 29 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8632 (mt-10) outliers start: 15 outliers final: 1 residues processed: 222 average time/residue: 0.3569 time to fit residues: 105.2106 Evaluate side-chains 118 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 116 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 128 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 148 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN B 312 HIS B 752 HIS C 122 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14194 Z= 0.187 Angle : 0.598 7.518 19480 Z= 0.320 Chirality : 0.040 0.159 2218 Planarity : 0.005 0.096 2319 Dihedral : 20.289 169.692 2483 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % 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: -1.20 (0.20), residues: 1575 helix: 0.12 (0.18), residues: 746 sheet: -1.62 (0.32), residues: 231 loop : -1.51 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 709 HIS 0.007 0.001 HIS C 231 PHE 0.015 0.002 PHE A 155 TYR 0.016 0.002 TYR A 145 ARG 0.012 0.001 ARG B 697 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.602 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: A 166 MET cc_start: 0.8895 (tpt) cc_final: 0.8582 (tpt) REVERT: A 306 MET cc_start: 0.8844 (ttm) cc_final: 0.8402 (ttt) REVERT: A 313 MET cc_start: 0.9494 (ttm) cc_final: 0.8854 (mmt) REVERT: A 348 LEU cc_start: 0.8644 (mt) cc_final: 0.7854 (mt) REVERT: A 368 MET cc_start: 0.9216 (mmp) cc_final: 0.8866 (mmp) REVERT: A 574 ASP cc_start: 0.8395 (p0) cc_final: 0.7949 (p0) REVERT: A 633 MET cc_start: 0.8126 (mtp) cc_final: 0.7697 (tpp) REVERT: A 674 MET cc_start: 0.8301 (mmp) cc_final: 0.7862 (mpp) REVERT: A 687 TYR cc_start: 0.8543 (m-80) cc_final: 0.8154 (m-80) REVERT: A 775 VAL cc_start: 0.8984 (t) cc_final: 0.8742 (t) REVERT: B 215 LEU cc_start: 0.8896 (pp) cc_final: 0.8234 (pp) REVERT: B 222 LEU cc_start: 0.8064 (mt) cc_final: 0.7828 (mt) REVERT: B 223 VAL cc_start: 0.8500 (t) cc_final: 0.8284 (p) REVERT: B 260 MET cc_start: 0.8416 (ttt) cc_final: 0.6873 (tmm) REVERT: B 302 MET cc_start: 0.9595 (ptm) cc_final: 0.9264 (ptm) REVERT: B 306 MET cc_start: 0.9059 (tpp) cc_final: 0.8715 (tpp) REVERT: B 313 MET cc_start: 0.8972 (tmm) cc_final: 0.8727 (tmm) REVERT: B 397 MET cc_start: 0.8747 (ttm) cc_final: 0.8446 (ttm) REVERT: B 421 ASP cc_start: 0.7632 (p0) cc_final: 0.7364 (p0) REVERT: C 29 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8201 (mt-10) REVERT: C 133 THR cc_start: 0.8835 (p) cc_final: 0.8593 (p) REVERT: C 146 GLU cc_start: 0.7803 (pt0) cc_final: 0.7324 (pm20) REVERT: C 160 PHE cc_start: 0.8289 (m-80) cc_final: 0.7968 (m-80) REVERT: C 233 ASP cc_start: 0.8149 (p0) cc_final: 0.7036 (t70) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.3325 time to fit residues: 64.2509 Evaluate side-chains 96 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 82 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 123 optimal weight: 0.8980 chunk 101 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 149 optimal weight: 7.9990 chunk 161 optimal weight: 9.9990 chunk 132 optimal weight: 0.7980 chunk 147 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 119 optimal weight: 0.7980 overall best weight: 1.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 GLN ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 734 GLN ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 GLN B 289 ASN B 544 GLN ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 714 ASN ** B 728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14194 Z= 0.212 Angle : 0.557 5.854 19480 Z= 0.299 Chirality : 0.038 0.187 2218 Planarity : 0.004 0.049 2319 Dihedral : 19.822 157.579 2483 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.15 % Allowed : 2.28 % Favored : 97.57 % 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: -0.31 (0.21), residues: 1575 helix: 0.98 (0.19), residues: 746 sheet: -1.15 (0.31), residues: 243 loop : -1.26 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 202 HIS 0.005 0.001 HIS B 752 PHE 0.013 0.002 PHE A 155 TYR 0.013 0.002 TYR C 255 ARG 0.005 0.000 ARG B 350 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 110 time to evaluate : 1.572 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: A 155 PHE cc_start: 0.8190 (t80) cc_final: 0.7801 (t80) REVERT: A 166 MET cc_start: 0.9011 (tpt) cc_final: 0.8763 (tpt) REVERT: A 187 MET cc_start: 0.8029 (tpt) cc_final: 0.7524 (tpp) REVERT: A 220 ARG cc_start: 0.3900 (ptt-90) cc_final: 0.3640 (ptt-90) REVERT: A 306 MET cc_start: 0.8589 (ttm) cc_final: 0.8335 (ttt) REVERT: A 313 MET cc_start: 0.9533 (ttm) cc_final: 0.8901 (mmt) REVERT: A 348 LEU cc_start: 0.9233 (mt) cc_final: 0.8734 (mt) REVERT: A 368 MET cc_start: 0.9254 (mmp) cc_final: 0.8967 (mmp) REVERT: A 574 ASP cc_start: 0.8242 (p0) cc_final: 0.7750 (p0) REVERT: A 633 MET cc_start: 0.8287 (mtp) cc_final: 0.7817 (tpp) REVERT: A 687 TYR cc_start: 0.8536 (m-80) cc_final: 0.8259 (m-80) REVERT: B 166 MET cc_start: 0.9030 (mmm) cc_final: 0.8796 (mmm) REVERT: B 222 LEU cc_start: 0.8245 (mt) cc_final: 0.8044 (mt) REVERT: B 269 MET cc_start: 0.8109 (ttm) cc_final: 0.7625 (ttm) REVERT: B 302 MET cc_start: 0.9706 (ptm) cc_final: 0.9421 (ptm) REVERT: B 313 MET cc_start: 0.9071 (tmm) cc_final: 0.8732 (tmm) REVERT: B 397 MET cc_start: 0.8732 (ttm) cc_final: 0.8471 (ttm) REVERT: B 624 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.8303 (mmt) REVERT: C 29 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8273 (mt-10) REVERT: C 160 PHE cc_start: 0.8346 (m-80) cc_final: 0.7970 (m-80) REVERT: C 168 PHE cc_start: 0.8674 (t80) cc_final: 0.8327 (t80) REVERT: C 233 ASP cc_start: 0.7865 (p0) cc_final: 0.7378 (t0) outliers start: 2 outliers final: 0 residues processed: 110 average time/residue: 0.3590 time to fit residues: 54.7146 Evaluate side-chains 88 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 147 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 78 optimal weight: 0.2980 chunk 141 optimal weight: 0.4980 chunk 42 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 ASN ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 GLN ** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14194 Z= 0.209 Angle : 0.555 8.796 19480 Z= 0.292 Chirality : 0.038 0.176 2218 Planarity : 0.004 0.057 2319 Dihedral : 19.493 135.446 2483 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.08 % Allowed : 2.50 % Favored : 97.42 % 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: 0.10 (0.21), residues: 1575 helix: 1.30 (0.19), residues: 751 sheet: -0.82 (0.33), residues: 229 loop : -1.12 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 202 HIS 0.005 0.001 HIS C 319 PHE 0.013 0.002 PHE B 725 TYR 0.013 0.002 TYR C 255 ARG 0.007 0.000 ARG A 449 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 1.576 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: A 155 PHE cc_start: 0.8383 (t80) cc_final: 0.7786 (t80) REVERT: A 166 MET cc_start: 0.8948 (tpt) cc_final: 0.8411 (tpt) REVERT: A 187 MET cc_start: 0.8256 (tpt) cc_final: 0.7714 (tpp) REVERT: A 306 MET cc_start: 0.8434 (ttm) cc_final: 0.8016 (ttt) REVERT: A 313 MET cc_start: 0.9485 (ttm) cc_final: 0.9001 (mmt) REVERT: A 348 LEU cc_start: 0.8932 (mt) cc_final: 0.8523 (mt) REVERT: A 574 ASP cc_start: 0.8269 (p0) cc_final: 0.7821 (p0) REVERT: A 633 MET cc_start: 0.8535 (mtp) cc_final: 0.7814 (tpp) REVERT: A 687 TYR cc_start: 0.8629 (m-80) cc_final: 0.8204 (m-80) REVERT: B 166 MET cc_start: 0.9081 (mmm) cc_final: 0.8796 (mmm) REVERT: B 302 MET cc_start: 0.9689 (ptm) cc_final: 0.9433 (ptm) REVERT: B 313 MET cc_start: 0.9230 (tmm) cc_final: 0.8841 (tmm) REVERT: B 397 MET cc_start: 0.8721 (ttm) cc_final: 0.8449 (ttm) REVERT: B 609 MET cc_start: 0.8563 (ptp) cc_final: 0.7917 (pmm) REVERT: B 624 MET cc_start: 0.9067 (mtt) cc_final: 0.8781 (mtt) REVERT: B 770 SER cc_start: 0.8243 (p) cc_final: 0.7946 (m) REVERT: C 29 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8083 (mt-10) REVERT: C 160 PHE cc_start: 0.8373 (m-80) cc_final: 0.7954 (m-80) REVERT: C 233 ASP cc_start: 0.7700 (p0) cc_final: 0.7238 (t70) outliers start: 1 outliers final: 0 residues processed: 98 average time/residue: 0.3310 time to fit residues: 45.8152 Evaluate side-chains 78 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 132 optimal weight: 0.0020 chunk 89 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 118 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 135 optimal weight: 10.0000 chunk 109 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 80 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 overall best weight: 1.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 326 GLN ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.5754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14194 Z= 0.227 Angle : 0.559 6.921 19480 Z= 0.297 Chirality : 0.038 0.165 2218 Planarity : 0.004 0.050 2319 Dihedral : 19.400 126.969 2483 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 19.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % 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: 0.28 (0.21), residues: 1575 helix: 1.42 (0.19), residues: 745 sheet: -0.64 (0.35), residues: 213 loop : -1.02 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 121 HIS 0.005 0.001 HIS A 760 PHE 0.013 0.002 PHE B 725 TYR 0.015 0.002 TYR C 257 ARG 0.007 0.001 ARG A 449 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 1.521 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 155 PHE cc_start: 0.8265 (t80) cc_final: 0.7896 (t80) REVERT: A 166 MET cc_start: 0.8987 (tpt) cc_final: 0.8610 (tpt) REVERT: A 187 MET cc_start: 0.8120 (tpt) cc_final: 0.7703 (tpp) REVERT: A 220 ARG cc_start: 0.2650 (ptt-90) cc_final: 0.2062 (ptt180) REVERT: A 306 MET cc_start: 0.8466 (ttm) cc_final: 0.8097 (ttt) REVERT: A 313 MET cc_start: 0.9474 (ttm) cc_final: 0.9039 (mmt) REVERT: A 348 LEU cc_start: 0.9131 (mt) cc_final: 0.8675 (mt) REVERT: A 507 LYS cc_start: 0.9587 (tmmt) cc_final: 0.9269 (tppt) REVERT: A 574 ASP cc_start: 0.8314 (p0) cc_final: 0.7913 (p0) REVERT: A 633 MET cc_start: 0.8550 (mtp) cc_final: 0.7878 (tpp) REVERT: A 687 TYR cc_start: 0.8742 (m-80) cc_final: 0.8174 (m-80) REVERT: B 166 MET cc_start: 0.9102 (mmm) cc_final: 0.8849 (mmm) REVERT: B 269 MET cc_start: 0.7617 (ttm) cc_final: 0.7295 (ttp) REVERT: B 302 MET cc_start: 0.9681 (ptm) cc_final: 0.9316 (ptm) REVERT: B 313 MET cc_start: 0.9266 (tmm) cc_final: 0.8863 (tmm) REVERT: B 397 MET cc_start: 0.8736 (ttm) cc_final: 0.8489 (ttm) REVERT: B 609 MET cc_start: 0.8548 (ptp) cc_final: 0.8305 (ptp) REVERT: B 759 MET cc_start: 0.8795 (mpp) cc_final: 0.8249 (mpp) REVERT: C 29 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8013 (mt-10) REVERT: C 160 PHE cc_start: 0.8457 (m-80) cc_final: 0.7713 (m-80) REVERT: C 168 PHE cc_start: 0.8944 (t80) cc_final: 0.8665 (t80) REVERT: C 233 ASP cc_start: 0.7820 (p0) cc_final: 0.7601 (t70) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.3231 time to fit residues: 39.3582 Evaluate side-chains 76 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 53 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 chunk 31 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 131 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN A 339 GLN ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 ASN ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.6427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14194 Z= 0.260 Angle : 0.604 7.492 19480 Z= 0.316 Chirality : 0.039 0.194 2218 Planarity : 0.004 0.047 2319 Dihedral : 19.408 116.274 2483 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 23.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.08 % Allowed : 1.59 % Favored : 98.33 % 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: 0.08 (0.21), residues: 1575 helix: 1.14 (0.19), residues: 757 sheet: -0.62 (0.36), residues: 213 loop : -1.05 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 121 HIS 0.007 0.001 HIS A 760 PHE 0.015 0.002 PHE B 725 TYR 0.015 0.002 TYR A 771 ARG 0.007 0.001 ARG C 158 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 90 time to evaluate : 1.510 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: A 166 MET cc_start: 0.9012 (tpt) cc_final: 0.8756 (tpt) REVERT: A 187 MET cc_start: 0.7903 (tpt) cc_final: 0.7415 (tpp) REVERT: A 220 ARG cc_start: 0.2269 (ptt-90) cc_final: 0.1595 (ptt180) REVERT: A 302 MET cc_start: 0.9139 (mtm) cc_final: 0.8678 (mtm) REVERT: A 306 MET cc_start: 0.8420 (ttm) cc_final: 0.7975 (ttt) REVERT: A 313 MET cc_start: 0.9473 (ttm) cc_final: 0.9150 (mmt) REVERT: A 348 LEU cc_start: 0.9241 (mt) cc_final: 0.8873 (mt) REVERT: A 617 MET cc_start: 0.7664 (ttm) cc_final: 0.7142 (mtt) REVERT: A 633 MET cc_start: 0.8837 (mtp) cc_final: 0.8163 (tpp) REVERT: A 687 TYR cc_start: 0.8969 (m-80) cc_final: 0.8265 (m-80) REVERT: A 739 MET cc_start: 0.6769 (ttt) cc_final: 0.5714 (tmm) REVERT: B 166 MET cc_start: 0.9160 (mmm) cc_final: 0.8866 (mmm) REVERT: B 302 MET cc_start: 0.9649 (ptm) cc_final: 0.9239 (ptm) REVERT: B 313 MET cc_start: 0.9340 (tmm) cc_final: 0.8903 (tmm) REVERT: B 609 MET cc_start: 0.8334 (ptp) cc_final: 0.8132 (ptp) REVERT: B 671 MET cc_start: 0.4989 (ttp) cc_final: 0.4337 (ptm) REVERT: B 692 MET cc_start: 0.8522 (mtp) cc_final: 0.8300 (mtp) REVERT: B 759 MET cc_start: 0.8898 (mpp) cc_final: 0.8225 (mpp) REVERT: B 770 SER cc_start: 0.8587 (p) cc_final: 0.8264 (m) REVERT: C 28 LYS cc_start: 0.9703 (mtpt) cc_final: 0.9501 (mtpp) REVERT: C 29 GLU cc_start: 0.8525 (mt-10) cc_final: 0.7916 (pt0) REVERT: C 160 PHE cc_start: 0.8691 (m-80) cc_final: 0.7957 (m-80) REVERT: C 168 PHE cc_start: 0.9256 (t80) cc_final: 0.8871 (t80) outliers start: 1 outliers final: 0 residues processed: 91 average time/residue: 0.3117 time to fit residues: 40.8847 Evaluate side-chains 72 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 152 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 89 optimal weight: 0.0170 chunk 133 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 158 optimal weight: 5.9990 chunk 98 optimal weight: 9.9990 chunk 96 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 HIS A 468 ASN ** A 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.6432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14194 Z= 0.152 Angle : 0.519 5.932 19480 Z= 0.271 Chirality : 0.038 0.171 2218 Planarity : 0.004 0.047 2319 Dihedral : 19.151 109.755 2483 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % 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: 0.48 (0.22), residues: 1575 helix: 1.50 (0.19), residues: 744 sheet: -0.51 (0.35), residues: 233 loop : -0.80 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 709 HIS 0.003 0.001 HIS B 682 PHE 0.014 0.001 PHE A 155 TYR 0.011 0.001 TYR A 145 ARG 0.006 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.374 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: A 166 MET cc_start: 0.8879 (tpt) cc_final: 0.8461 (tpt) REVERT: A 187 MET cc_start: 0.7759 (tpt) cc_final: 0.7251 (tpp) REVERT: A 302 MET cc_start: 0.8718 (mtm) cc_final: 0.8507 (mtm) REVERT: A 306 MET cc_start: 0.8595 (ttm) cc_final: 0.8157 (ttt) REVERT: A 313 MET cc_start: 0.9481 (ttm) cc_final: 0.9108 (mmt) REVERT: A 348 LEU cc_start: 0.9091 (mt) cc_final: 0.8547 (mt) REVERT: A 368 MET cc_start: 0.9243 (mmp) cc_final: 0.8924 (mmp) REVERT: A 624 MET cc_start: 0.7116 (mmm) cc_final: 0.6228 (mmt) REVERT: A 633 MET cc_start: 0.8474 (mtp) cc_final: 0.7822 (tpp) REVERT: A 687 TYR cc_start: 0.9042 (m-80) cc_final: 0.8362 (m-80) REVERT: A 739 MET cc_start: 0.6892 (ttt) cc_final: 0.5697 (tmm) REVERT: B 166 MET cc_start: 0.9159 (mmm) cc_final: 0.8877 (mmm) REVERT: B 187 MET cc_start: 0.8194 (mmt) cc_final: 0.7675 (mmm) REVERT: B 289 ASN cc_start: 0.8078 (m-40) cc_final: 0.7857 (t0) REVERT: B 302 MET cc_start: 0.9622 (ptm) cc_final: 0.9308 (ptm) REVERT: B 313 MET cc_start: 0.9328 (tmm) cc_final: 0.8892 (tmm) REVERT: B 739 MET cc_start: 0.7911 (tpp) cc_final: 0.7707 (tpp) REVERT: B 759 MET cc_start: 0.8938 (mpp) cc_final: 0.8371 (mpp) REVERT: C 28 LYS cc_start: 0.9678 (mtpt) cc_final: 0.9390 (mtpp) REVERT: C 29 GLU cc_start: 0.8555 (mt-10) cc_final: 0.7923 (pt0) REVERT: C 160 PHE cc_start: 0.8587 (m-80) cc_final: 0.8048 (m-80) REVERT: C 168 PHE cc_start: 0.9205 (t80) cc_final: 0.8794 (t80) REVERT: C 189 LEU cc_start: 0.8987 (tp) cc_final: 0.8770 (tp) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.3261 time to fit residues: 40.8213 Evaluate side-chains 73 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 97 optimal weight: 9.9990 chunk 63 optimal weight: 0.3980 chunk 94 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 31 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 124 optimal weight: 7.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 GLN A 468 ASN ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.7123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14194 Z= 0.318 Angle : 0.663 7.700 19480 Z= 0.348 Chirality : 0.040 0.228 2218 Planarity : 0.005 0.044 2319 Dihedral : 19.470 93.093 2483 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 26.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.21), residues: 1575 helix: 0.94 (0.19), residues: 757 sheet: -0.68 (0.37), residues: 217 loop : -1.01 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 436 HIS 0.007 0.001 HIS A 760 PHE 0.018 0.002 PHE B 725 TYR 0.023 0.002 TYR C 323 ARG 0.014 0.001 ARG C 200 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.748 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 166 MET cc_start: 0.9120 (tpt) cc_final: 0.8689 (tpt) REVERT: A 220 ARG cc_start: 0.3523 (ptt180) cc_final: 0.3084 (ptt180) REVERT: A 302 MET cc_start: 0.8380 (mtm) cc_final: 0.8000 (mtm) REVERT: A 306 MET cc_start: 0.8459 (ttm) cc_final: 0.8057 (ttt) REVERT: A 348 LEU cc_start: 0.8730 (mt) cc_final: 0.8157 (mt) REVERT: A 368 MET cc_start: 0.9310 (mmp) cc_final: 0.9020 (mmp) REVERT: A 624 MET cc_start: 0.7226 (mmm) cc_final: 0.5876 (mmt) REVERT: A 633 MET cc_start: 0.8593 (mtp) cc_final: 0.7960 (tpp) REVERT: B 166 MET cc_start: 0.9152 (mmm) cc_final: 0.8875 (mmm) REVERT: B 302 MET cc_start: 0.9613 (ptm) cc_final: 0.9238 (ptm) REVERT: B 313 MET cc_start: 0.9388 (tmm) cc_final: 0.9004 (tmm) REVERT: B 609 MET cc_start: 0.8613 (ptp) cc_final: 0.8093 (pmm) REVERT: B 624 MET cc_start: 0.8962 (mtt) cc_final: 0.8572 (mtt) REVERT: B 646 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8221 (mp0) REVERT: B 692 MET cc_start: 0.8671 (mtp) cc_final: 0.8423 (mtp) REVERT: B 739 MET cc_start: 0.8149 (tpp) cc_final: 0.7577 (tpp) REVERT: B 759 MET cc_start: 0.8829 (mpp) cc_final: 0.8197 (mpp) REVERT: B 770 SER cc_start: 0.8731 (p) cc_final: 0.8414 (m) REVERT: C 28 LYS cc_start: 0.9717 (mtpt) cc_final: 0.9459 (mtpp) REVERT: C 29 GLU cc_start: 0.8559 (mt-10) cc_final: 0.7986 (pt0) REVERT: C 160 PHE cc_start: 0.8789 (m-80) cc_final: 0.8006 (m-80) REVERT: C 168 PHE cc_start: 0.9262 (t80) cc_final: 0.8995 (t80) REVERT: C 189 LEU cc_start: 0.9123 (tp) cc_final: 0.8881 (tp) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.3064 time to fit residues: 35.3643 Evaluate side-chains 68 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 143 optimal weight: 0.7980 chunk 151 optimal weight: 4.9990 chunk 138 optimal weight: 10.0000 chunk 147 optimal weight: 0.5980 chunk 88 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 GLN A 468 ASN ** A 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 ASN B 370 HIS ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.7009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14194 Z= 0.158 Angle : 0.540 5.895 19480 Z= 0.283 Chirality : 0.039 0.201 2218 Planarity : 0.004 0.070 2319 Dihedral : 19.148 88.614 2483 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: 0.28 (0.21), residues: 1575 helix: 1.34 (0.19), residues: 747 sheet: -0.50 (0.37), residues: 208 loop : -0.96 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 709 HIS 0.004 0.001 HIS B 682 PHE 0.013 0.001 PHE A 155 TYR 0.020 0.001 TYR A 563 ARG 0.010 0.000 ARG C 200 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.693 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 166 MET cc_start: 0.8876 (tpt) cc_final: 0.8446 (tpt) REVERT: A 220 ARG cc_start: 0.3226 (ptt180) cc_final: 0.2870 (ptt180) REVERT: A 302 MET cc_start: 0.8746 (mtm) cc_final: 0.8482 (mtm) REVERT: A 306 MET cc_start: 0.8400 (ttm) cc_final: 0.7951 (ttt) REVERT: A 348 LEU cc_start: 0.8793 (mt) cc_final: 0.8237 (mt) REVERT: A 368 MET cc_start: 0.9273 (mmp) cc_final: 0.8916 (mmp) REVERT: A 624 MET cc_start: 0.7119 (mmm) cc_final: 0.6133 (mmt) REVERT: A 633 MET cc_start: 0.8500 (mtp) cc_final: 0.7966 (tpp) REVERT: A 687 TYR cc_start: 0.9131 (m-80) cc_final: 0.8407 (m-80) REVERT: B 166 MET cc_start: 0.9106 (mmm) cc_final: 0.8888 (mmm) REVERT: B 187 MET cc_start: 0.8422 (mmt) cc_final: 0.7840 (mmm) REVERT: B 302 MET cc_start: 0.9619 (ptm) cc_final: 0.9349 (ptm) REVERT: B 461 ASP cc_start: 0.8377 (m-30) cc_final: 0.8092 (m-30) REVERT: B 609 MET cc_start: 0.8291 (ptp) cc_final: 0.7943 (pmm) REVERT: B 624 MET cc_start: 0.8843 (mtt) cc_final: 0.8447 (mtt) REVERT: B 646 GLU cc_start: 0.8681 (mt-10) cc_final: 0.7434 (mp0) REVERT: B 739 MET cc_start: 0.8242 (tpp) cc_final: 0.7827 (tpp) REVERT: B 759 MET cc_start: 0.9083 (mpp) cc_final: 0.8715 (mpp) REVERT: B 770 SER cc_start: 0.8314 (p) cc_final: 0.7983 (m) REVERT: C 28 LYS cc_start: 0.9695 (mtpt) cc_final: 0.9443 (mtpp) REVERT: C 29 GLU cc_start: 0.8403 (mt-10) cc_final: 0.7920 (pt0) REVERT: C 160 PHE cc_start: 0.8559 (m-10) cc_final: 0.7992 (m-80) REVERT: C 168 PHE cc_start: 0.9124 (t80) cc_final: 0.8813 (t80) REVERT: C 189 LEU cc_start: 0.8948 (tp) cc_final: 0.8699 (tp) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.3038 time to fit residues: 37.2757 Evaluate side-chains 73 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 96 optimal weight: 0.7980 chunk 155 optimal weight: 8.9990 chunk 95 optimal weight: 9.9990 chunk 73 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 chunk 163 optimal weight: 7.9990 chunk 150 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 13 optimal weight: 0.2980 chunk 100 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN ** A 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.7226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14194 Z= 0.207 Angle : 0.569 11.970 19480 Z= 0.297 Chirality : 0.038 0.189 2218 Planarity : 0.004 0.071 2319 Dihedral : 19.210 89.520 2483 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.08 % Allowed : 0.23 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.21), residues: 1575 helix: 1.29 (0.19), residues: 757 sheet: -0.53 (0.37), residues: 217 loop : -1.01 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.005 0.001 HIS A 760 PHE 0.013 0.002 PHE A 155 TYR 0.018 0.002 TYR A 563 ARG 0.011 0.001 ARG C 200 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 1.442 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: A 166 MET cc_start: 0.9011 (tpt) cc_final: 0.8572 (tpt) REVERT: A 220 ARG cc_start: 0.3389 (ptt180) cc_final: 0.2955 (ptt180) REVERT: A 302 MET cc_start: 0.8707 (mtm) cc_final: 0.8409 (mtm) REVERT: A 306 MET cc_start: 0.8467 (ttm) cc_final: 0.8084 (ttt) REVERT: A 313 MET cc_start: 0.8852 (mpp) cc_final: 0.8592 (mmm) REVERT: A 348 LEU cc_start: 0.8799 (mt) cc_final: 0.8260 (mt) REVERT: A 368 MET cc_start: 0.9321 (mmp) cc_final: 0.8921 (mmp) REVERT: A 624 MET cc_start: 0.7121 (mmm) cc_final: 0.6069 (mmt) REVERT: A 633 MET cc_start: 0.8546 (mtp) cc_final: 0.7988 (tpp) REVERT: A 687 TYR cc_start: 0.9051 (m-80) cc_final: 0.8323 (m-80) REVERT: B 166 MET cc_start: 0.9123 (mmm) cc_final: 0.8906 (mmm) REVERT: B 187 MET cc_start: 0.8453 (mmt) cc_final: 0.7990 (mmm) REVERT: B 302 MET cc_start: 0.9581 (ptm) cc_final: 0.9262 (ptm) REVERT: B 313 MET cc_start: 0.9198 (tmm) cc_final: 0.8907 (tmm) REVERT: B 461 ASP cc_start: 0.8411 (m-30) cc_final: 0.8196 (m-30) REVERT: B 609 MET cc_start: 0.8318 (ptp) cc_final: 0.7964 (pmm) REVERT: B 624 MET cc_start: 0.8783 (mtt) cc_final: 0.8306 (mtt) REVERT: B 646 GLU cc_start: 0.8709 (mt-10) cc_final: 0.7501 (mp0) REVERT: B 759 MET cc_start: 0.8933 (mpp) cc_final: 0.8386 (mpp) REVERT: C 28 LYS cc_start: 0.9704 (mtpt) cc_final: 0.9462 (mtpp) REVERT: C 29 GLU cc_start: 0.8475 (mt-10) cc_final: 0.7976 (pt0) REVERT: C 160 PHE cc_start: 0.8597 (m-10) cc_final: 0.7972 (m-80) REVERT: C 168 PHE cc_start: 0.9203 (t80) cc_final: 0.8886 (t80) REVERT: C 189 LEU cc_start: 0.9030 (tp) cc_final: 0.8741 (tp) outliers start: 1 outliers final: 0 residues processed: 83 average time/residue: 0.2887 time to fit residues: 35.2569 Evaluate side-chains 73 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 103 optimal weight: 6.9990 chunk 138 optimal weight: 9.9990 chunk 39 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 133 optimal weight: 0.0170 chunk 16 optimal weight: 0.0030 chunk 24 optimal weight: 0.9980 overall best weight: 1.1630 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 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 = 0.3396 r_free = 0.3396 target = 0.048341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.036583 restraints weight = 124683.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.037828 restraints weight = 78921.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.038710 restraints weight = 56079.117| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.7292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14194 Z= 0.171 Angle : 0.547 10.779 19480 Z= 0.285 Chirality : 0.039 0.197 2218 Planarity : 0.004 0.064 2319 Dihedral : 19.079 89.233 2483 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.08 % Allowed : 0.08 % Favored : 99.85 % 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: 0.36 (0.21), residues: 1575 helix: 1.42 (0.19), residues: 753 sheet: -0.52 (0.37), residues: 213 loop : -0.94 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 709 HIS 0.004 0.001 HIS B 682 PHE 0.014 0.001 PHE A 155 TYR 0.018 0.001 TYR A 563 ARG 0.010 0.000 ARG C 200 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2322.12 seconds wall clock time: 60 minutes 37.84 seconds (3637.84 seconds total)