Starting phenix.real_space_refine on Sun Dec 10 08:03:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aib_11794/12_2023/7aib_11794_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aib_11794/12_2023/7aib_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_11794/12_2023/7aib_11794.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aib_11794/12_2023/7aib_11794.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aib_11794/12_2023/7aib_11794_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aib_11794/12_2023/7aib_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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 7.27, per 1000 atoms: 0.53 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: 5.76 Conformation dependent library (CDL) restraints added in 2.3 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: 7.03 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: 4.97 Time building geometry restraints manager: 6.15 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: 0.580 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: 2.280 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 44.130 Find NCS groups from input model: 0.710 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.990 ------------------------------------------------------------------------------- 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 : 1.521 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 1 residues processed: 222 average time/residue: 0.3687 time to fit residues: 108.5048 Evaluate side-chains 111 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 1.562 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1563 time to fit residues: 2.3509 ------------------------------------------------------------------------------- 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: 0.9990 chunk 124 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 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: 0.9990 chunk 95 optimal weight: 0.9980 chunk 148 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14194 Z= 0.181 Angle : 0.598 7.939 19480 Z= 0.321 Chirality : 0.040 0.166 2218 Planarity : 0.005 0.101 2319 Dihedral : 20.317 169.447 2483 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % 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: -1.26 (0.20), residues: 1575 helix: 0.05 (0.18), residues: 746 sheet: -1.58 (0.32), residues: 230 loop : -1.53 (0.24), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 709 HIS 0.010 0.001 HIS B 312 PHE 0.016 0.002 PHE A 155 TYR 0.014 0.002 TYR A 145 ARG 0.007 0.001 ARG B 350 *********************** 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 138 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.537 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 outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.3488 time to fit residues: 65.7721 Evaluate side-chains 86 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.595 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8713 ------------------------------------------------------------------------------- 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: 4.9990 chunk 46 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 149 optimal weight: 8.9990 chunk 161 optimal weight: 9.9990 chunk 132 optimal weight: 0.0980 chunk 147 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 119 optimal weight: 0.5980 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 ** A 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 223 GLN ** 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: 0.7431 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14194 Z= 0.217 Angle : 0.568 5.889 19480 Z= 0.304 Chirality : 0.039 0.176 2218 Planarity : 0.004 0.049 2319 Dihedral : 19.854 158.764 2483 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.15 % Allowed : 2.43 % 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: -0.43 (0.21), residues: 1575 helix: 0.85 (0.19), residues: 748 sheet: -1.15 (0.32), residues: 228 loop : -1.31 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 709 HIS 0.008 0.001 HIS A 760 PHE 0.014 0.002 PHE A 155 TYR 0.013 0.002 TYR C 255 ARG 0.013 0.001 ARG A 656 *********************** 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 114 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 112 time to evaluate : 1.608 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 outliers start: 2 outliers final: 0 residues processed: 112 average time/residue: 0.3654 time to fit residues: 56.3292 Evaluate side-chains 84 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 1.567 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0873 ------------------------------------------------------------------------------- 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: 4.9990 chunk 112 optimal weight: 0.5980 chunk 77 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 78 optimal weight: 0.0670 chunk 141 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 overall best weight: 1.7122 ------------------------------------------------------------------------------- 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** ** 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: 0.7479 moved from start: 0.5142 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= 0.209 Angle : 0.551 6.163 19480 Z= 0.291 Chirality : 0.038 0.240 2218 Planarity : 0.004 0.050 2319 Dihedral : 19.503 139.383 2483 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % 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: 0.00 (0.21), residues: 1575 helix: 1.17 (0.19), residues: 757 sheet: -1.02 (0.33), residues: 238 loop : -1.04 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 202 HIS 0.006 0.001 HIS A 760 PHE 0.020 0.002 PHE B 725 TYR 0.013 0.002 TYR C 255 ARG 0.008 0.000 ARG A 656 *********************** 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 98 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 97 average time/residue: 0.3462 time to fit residues: 47.7500 Evaluate side-chains 68 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.678 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0643 ------------------------------------------------------------------------------- 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: 0.0570 chunk 89 optimal weight: 0.7980 chunk 2 optimal weight: 8.9990 chunk 118 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 135 optimal weight: 9.9990 chunk 109 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 80 optimal weight: 1.9990 chunk 142 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 overall best weight: 3.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN A 326 GLN A 339 GLN ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 717 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 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.6369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14194 Z= 0.349 Angle : 0.706 11.087 19480 Z= 0.369 Chirality : 0.041 0.178 2218 Planarity : 0.005 0.052 2319 Dihedral : 19.785 145.496 2483 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 28.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.08 % Allowed : 2.43 % Favored : 97.50 % 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: -0.50 (0.21), residues: 1575 helix: 0.57 (0.18), residues: 762 sheet: -0.76 (0.36), residues: 200 loop : -1.25 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 121 HIS 0.008 0.001 HIS A 760 PHE 0.020 0.002 PHE B 725 TYR 0.035 0.002 TYR C 257 ARG 0.009 0.001 ARG C 177 *********************** 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 88 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 88 average time/residue: 0.3242 time to fit residues: 41.3803 Evaluate side-chains 67 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 1.675 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1406 ------------------------------------------------------------------------------- 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: 0.5980 chunk 142 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 13 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 83 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 683 ASN ** B 171 GLN ** 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 324 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: 0.7545 moved from start: 0.6346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14194 Z= 0.186 Angle : 0.554 6.843 19480 Z= 0.290 Chirality : 0.038 0.179 2218 Planarity : 0.004 0.047 2319 Dihedral : 19.450 136.638 2483 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 19.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % 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: -0.02 (0.21), residues: 1575 helix: 1.02 (0.19), residues: 747 sheet: -0.68 (0.37), residues: 206 loop : -1.00 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 229 HIS 0.003 0.001 HIS A 760 PHE 0.017 0.001 PHE B 725 TYR 0.016 0.001 TYR C 257 ARG 0.007 0.000 ARG A 319 *********************** 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 89 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 1.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.3322 time to fit residues: 42.4485 Evaluate side-chains 67 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 1.620 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1747 ------------------------------------------------------------------------------- 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: 0.0030 chunk 17 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 96 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- 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 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 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.6719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14194 Z= 0.215 Angle : 0.579 6.282 19480 Z= 0.302 Chirality : 0.038 0.167 2218 Planarity : 0.004 0.045 2319 Dihedral : 19.459 125.255 2483 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 21.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % 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: -0.04 (0.21), residues: 1575 helix: 1.01 (0.19), residues: 748 sheet: -0.52 (0.38), residues: 194 loop : -1.06 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 310 HIS 0.004 0.001 HIS A 760 PHE 0.014 0.002 PHE B 725 TYR 0.014 0.002 TYR A 771 ARG 0.005 0.001 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 83 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.601 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 outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.3402 time to fit residues: 40.0587 Evaluate side-chains 68 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.521 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9492 ------------------------------------------------------------------------------- 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: 10.0000 chunk 63 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 chunk 31 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 78 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** 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 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.6881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14194 Z= 0.193 Angle : 0.557 6.884 19480 Z= 0.289 Chirality : 0.038 0.215 2218 Planarity : 0.004 0.045 2319 Dihedral : 19.353 114.371 2483 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 20.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % 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: 0.09 (0.21), residues: 1575 helix: 1.08 (0.19), residues: 752 sheet: -0.47 (0.37), residues: 205 loop : -0.95 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 229 HIS 0.004 0.001 HIS B 682 PHE 0.013 0.002 PHE B 725 TYR 0.011 0.001 TYR B 623 ARG 0.007 0.000 ARG C 273 *********************** 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 : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.3239 time to fit residues: 36.7139 Evaluate side-chains 61 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 1.452 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8984 ------------------------------------------------------------------------------- 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: 4.9990 chunk 151 optimal weight: 7.9990 chunk 138 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 64 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 133 optimal weight: 0.9990 chunk 139 optimal weight: 9.9990 chunk 146 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 GLN ** 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 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 GLN ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.7347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14194 Z= 0.274 Angle : 0.641 8.039 19480 Z= 0.332 Chirality : 0.039 0.182 2218 Planarity : 0.004 0.043 2319 Dihedral : 19.451 88.973 2483 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 26.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % 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: 0.87 (0.19), residues: 748 sheet: -0.49 (0.38), residues: 203 loop : -0.95 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.004 0.001 HIS A 760 PHE 0.019 0.002 PHE B 725 TYR 0.016 0.002 TYR A 771 ARG 0.011 0.001 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 75 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 1.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.3318 time to fit residues: 37.2166 Evaluate side-chains 60 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.770 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3676 ------------------------------------------------------------------------------- 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: 3.9990 chunk 155 optimal weight: 8.9990 chunk 95 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 163 optimal weight: 7.9990 chunk 150 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 GLN ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 HIS ** B 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.8084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 14194 Z= 0.378 Angle : 0.767 10.362 19480 Z= 0.398 Chirality : 0.042 0.168 2218 Planarity : 0.006 0.109 2319 Dihedral : 19.664 88.032 2483 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 32.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % 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: -0.73 (0.21), residues: 1575 helix: 0.23 (0.18), residues: 743 sheet: -0.88 (0.35), residues: 208 loop : -1.10 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 239 HIS 0.006 0.002 HIS A 760 PHE 0.026 0.003 PHE C 168 TYR 0.024 0.002 TYR A 563 ARG 0.018 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 80 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.2404 time to fit residues: 28.1036 Evaluate side-chains 61 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 1.234 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5160 ------------------------------------------------------------------------------- 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: 10.0000 chunk 138 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 214 ASN ** A 626 GLN ** 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 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 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 = 0.3397 r_free = 0.3397 target = 0.048289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.036329 restraints weight = 137047.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.037511 restraints weight = 86019.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.038339 restraints weight = 61507.300| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.7920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14194 Z= 0.203 Angle : 0.610 11.016 19480 Z= 0.317 Chirality : 0.040 0.181 2218 Planarity : 0.005 0.079 2319 Dihedral : 19.447 89.582 2483 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 22.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % 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: -0.32 (0.21), residues: 1575 helix: 0.74 (0.19), residues: 744 sheet: -0.64 (0.36), residues: 204 loop : -1.15 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 202 HIS 0.006 0.001 HIS B 682 PHE 0.029 0.002 PHE C 168 TYR 0.021 0.002 TYR A 563 ARG 0.012 0.001 ARG C 200 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2399.41 seconds wall clock time: 48 minutes 34.70 seconds (2914.70 seconds total)