Starting phenix.real_space_refine (version: dev) on Thu May 12 23:45:04 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxj_21440/05_2022/6vxj_21440_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxj_21440/05_2022/6vxj_21440.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxj_21440/05_2022/6vxj_21440_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxj_21440/05_2022/6vxj_21440_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxj_21440/05_2022/6vxj_21440_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxj_21440/05_2022/6vxj_21440.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxj_21440/05_2022/6vxj_21440.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxj_21440/05_2022/6vxj_21440_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxj_21440/05_2022/6vxj_21440_updated.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 8895 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4405 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 18, 'TRANS': 547} Chain breaks: 3 Chain: "B" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4405 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 18, 'TRANS': 547} Chain breaks: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'RS4': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.30, per 1000 atoms: 0.60 Number of scatterers: 8895 At special positions: 0 Unit cell: (104.55, 77.49, 126.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1589 8.00 N 1454 7.00 C 5794 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 608 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS B 603 " distance=2.03 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.03 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: 3.73 Conformation dependent library (CDL) restraints added in 1.5 seconds 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2092 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 4 sheets defined 48.3% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 86 through 93 removed outlier: 3.652A pdb=" N LEU A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 120 removed outlier: 4.468A pdb=" N LYS A 118 " --> pdb=" O ALA A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 146 removed outlier: 4.164A pdb=" N SER A 143 " --> pdb=" O ASN A 139 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 167 removed outlier: 5.084A pdb=" N GLU A 159 " --> pdb=" O HIS A 155 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ARG A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLN A 166 " --> pdb=" O ASN A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 200 removed outlier: 3.733A pdb=" N GLU A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU A 200 " --> pdb=" O ILE A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 234 removed outlier: 3.599A pdb=" N LEU A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLN A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 279 removed outlier: 4.215A pdb=" N GLU A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER A 279 " --> pdb=" O GLY A 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 274 through 279' Processing helix chain 'A' and resid 290 through 293 No H-bonds generated for 'chain 'A' and resid 290 through 293' Processing helix chain 'A' and resid 296 through 299 No H-bonds generated for 'chain 'A' and resid 296 through 299' Processing helix chain 'A' and resid 331 through 335 removed outlier: 4.185A pdb=" N ILE A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 331 through 335' Processing helix chain 'A' and resid 342 through 353 Processing helix chain 'A' and resid 373 through 388 removed outlier: 3.727A pdb=" N TRP A 379 " --> pdb=" O HIS A 375 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 412 Processing helix chain 'A' and resid 420 through 444 removed outlier: 4.188A pdb=" N ILE A 423 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N GLN A 424 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG A 426 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ALA A 427 " --> pdb=" O GLN A 424 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL A 429 " --> pdb=" O ARG A 426 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU A 430 " --> pdb=" O ALA A 427 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU A 433 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 435 " --> pdb=" O PHE A 432 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN A 436 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS A 438 " --> pdb=" O THR A 435 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER A 440 " --> pdb=" O GLN A 437 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER A 441 " --> pdb=" O CYS A 438 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER A 443 " --> pdb=" O SER A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 460 removed outlier: 3.849A pdb=" N GLU A 458 " --> pdb=" O LEU A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 477 removed outlier: 3.583A pdb=" N LEU A 474 " --> pdb=" O PHE A 470 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER A 476 " --> pdb=" O GLY A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 497 removed outlier: 4.174A pdb=" N CYS A 491 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE A 492 " --> pdb=" O ILE A 488 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N MET A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 526 removed outlier: 3.500A pdb=" N PHE A 511 " --> pdb=" O PHE A 507 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET A 514 " --> pdb=" O MET A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 550 removed outlier: 4.082A pdb=" N PHE A 547 " --> pdb=" O ILE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 560 No H-bonds generated for 'chain 'A' and resid 558 through 560' Processing helix chain 'A' and resid 566 through 569 Processing helix chain 'A' and resid 573 through 583 removed outlier: 3.507A pdb=" N GLY A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 616 removed outlier: 3.514A pdb=" N VAL A 615 " --> pdb=" O GLU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 649 removed outlier: 3.904A pdb=" N TRP A 627 " --> pdb=" O PRO A 623 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ASN A 629 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N HIS A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 639 " --> pdb=" O CYS A 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 93 removed outlier: 3.652A pdb=" N LEU B 90 " --> pdb=" O LYS B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 120 removed outlier: 4.469A pdb=" N LYS B 118 " --> pdb=" O ALA B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 146 removed outlier: 4.165A pdb=" N SER B 143 " --> pdb=" O ASN B 139 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B 146 " --> pdb=" O PHE B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 167 removed outlier: 5.084A pdb=" N GLU B 159 " --> pdb=" O HIS B 155 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ARG B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE B 161 " --> pdb=" O LYS B 157 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLN B 166 " --> pdb=" O ASN B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 200 removed outlier: 3.733A pdb=" N GLU B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU B 200 " --> pdb=" O ILE B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 234 removed outlier: 3.599A pdb=" N LEU B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N GLN B 234 " --> pdb=" O ARG B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 279 removed outlier: 4.215A pdb=" N GLU B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 274 through 279' Processing helix chain 'B' and resid 290 through 293 No H-bonds generated for 'chain 'B' and resid 290 through 293' Processing helix chain 'B' and resid 296 through 299 No H-bonds generated for 'chain 'B' and resid 296 through 299' Processing helix chain 'B' and resid 331 through 335 removed outlier: 4.185A pdb=" N ILE B 335 " --> pdb=" O LYS B 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 331 through 335' Processing helix chain 'B' and resid 342 through 353 Processing helix chain 'B' and resid 373 through 388 removed outlier: 3.726A pdb=" N TRP B 379 " --> pdb=" O HIS B 375 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 412 Processing helix chain 'B' and resid 423 through 444 removed outlier: 4.027A pdb=" N THR B 434 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N VAL B 442 " --> pdb=" O CYS B 438 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N SER B 443 " --> pdb=" O PHE B 439 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ALA B 444 " --> pdb=" O SER B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 460 removed outlier: 3.849A pdb=" N GLU B 458 " --> pdb=" O LEU B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 477 removed outlier: 3.583A pdb=" N LEU B 474 " --> pdb=" O PHE B 470 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU B 475 " --> pdb=" O LEU B 471 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER B 476 " --> pdb=" O GLY B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 497 removed outlier: 4.174A pdb=" N CYS B 491 " --> pdb=" O ILE B 487 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE B 492 " --> pdb=" O ILE B 488 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N PHE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N MET B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 526 removed outlier: 3.641A pdb=" N MET B 514 " --> pdb=" O MET B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 550 removed outlier: 4.080A pdb=" N PHE B 547 " --> pdb=" O ILE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 560 No H-bonds generated for 'chain 'B' and resid 558 through 560' Processing helix chain 'B' and resid 566 through 569 Processing helix chain 'B' and resid 573 through 583 removed outlier: 3.507A pdb=" N GLY B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 616 removed outlier: 3.514A pdb=" N VAL B 615 " --> pdb=" O GLU B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 649 removed outlier: 3.904A pdb=" N TRP B 627 " --> pdb=" O PRO B 623 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ASN B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N HIS B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE B 639 " --> pdb=" O CYS B 635 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 37 through 40 removed outlier: 3.655A pdb=" N ASP A 105 " --> pdb=" O HIS A 40 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 263 through 268 removed outlier: 6.800A pdb=" N LEU A 258 " --> pdb=" O MET A 265 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N HIS A 267 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU A 256 " --> pdb=" O HIS A 267 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ILE A 238 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ILE A 78 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N PHE A 240 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N GLY A 80 " --> pdb=" O PHE A 240 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLY A 122 " --> pdb=" O PHE A 208 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 37 through 40 removed outlier: 3.655A pdb=" N ASP B 105 " --> pdb=" O HIS B 40 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 263 through 268 removed outlier: 6.802A pdb=" N LEU B 258 " --> pdb=" O MET B 265 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N HIS B 267 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU B 256 " --> pdb=" O HIS B 267 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ILE B 238 " --> pdb=" O ASN B 76 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ILE B 78 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N PHE B 240 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N GLY B 80 " --> pdb=" O PHE B 240 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLY B 122 " --> pdb=" O PHE B 208 " (cutoff:3.500A) 300 hydrogen bonds defined for protein. 846 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.45 Time building geometry restraints manager: 4.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2621 1.34 - 1.45: 1656 1.45 - 1.57: 4718 1.57 - 1.69: 0 1.69 - 1.81: 94 Bond restraints: 9089 Sorted by residual: bond pdb=" C20 RS4 B 701 " pdb=" C21 RS4 B 701 " ideal model delta sigma weight residual 0.000 1.474 -1.474 2.00e-02 2.50e+03 5.43e+03 bond pdb=" C11 RS4 B 701 " pdb=" C17 RS4 B 701 " ideal model delta sigma weight residual 2.560 1.464 1.096 2.00e-02 2.50e+03 3.01e+03 bond pdb=" C10 RS4 B 701 " pdb=" C11 RS4 B 701 " ideal model delta sigma weight residual 0.646 1.460 -0.814 2.00e-02 2.50e+03 1.66e+03 bond pdb=" C7 RS4 B 701 " pdb=" C8 RS4 B 701 " ideal model delta sigma weight residual 2.298 1.518 0.780 2.00e-02 2.50e+03 1.52e+03 bond pdb=" C21 RS4 B 701 " pdb=" C24 RS4 B 701 " ideal model delta sigma weight residual 2.192 1.501 0.691 2.00e-02 2.50e+03 1.19e+03 ... (remaining 9084 not shown) Histogram of bond angle deviations from ideal: 96.91 - 104.31: 123 104.31 - 111.72: 4099 111.72 - 119.12: 3280 119.12 - 126.52: 4710 126.52 - 133.93: 106 Bond angle restraints: 12318 Sorted by residual: angle pdb=" C22 RS4 B 701 " pdb=" C21 RS4 B 701 " pdb=" C24 RS4 B 701 " ideal model delta sigma weight residual 63.71 120.40 -56.69 3.00e+00 1.11e-01 3.57e+02 angle pdb=" C19 RS4 B 701 " pdb=" C17 RS4 B 701 " pdb=" N18 RS4 B 701 " ideal model delta sigma weight residual 79.97 125.37 -45.40 3.00e+00 1.11e-01 2.29e+02 angle pdb=" C11 RS4 B 701 " pdb=" C17 RS4 B 701 " pdb=" N18 RS4 B 701 " ideal model delta sigma weight residual 70.48 108.45 -37.97 3.00e+00 1.11e-01 1.60e+02 angle pdb=" C11 RS4 B 701 " pdb=" C17 RS4 B 701 " pdb=" C19 RS4 B 701 " ideal model delta sigma weight residual 150.45 126.18 24.27 3.00e+00 1.11e-01 6.55e+01 angle pdb=" C21 RS4 B 701 " pdb=" C20 RS4 B 701 " pdb=" C25 RS4 B 701 " ideal model delta sigma weight residual 98.26 121.86 -23.60 3.00e+00 1.11e-01 6.19e+01 ... (remaining 12313 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 4642 17.33 - 34.66: 509 34.66 - 51.99: 156 51.99 - 69.32: 28 69.32 - 86.65: 13 Dihedral angle restraints: 5348 sinusoidal: 2088 harmonic: 3260 Sorted by residual: dihedral pdb=" CB CYS A 603 " pdb=" SG CYS A 603 " pdb=" SG CYS B 603 " pdb=" CB CYS B 603 " ideal model delta sinusoidal sigma weight residual 93.00 8.05 84.95 1 1.00e+01 1.00e-02 8.75e+01 dihedral pdb=" CA LEU B 484 " pdb=" C LEU B 484 " pdb=" N PRO B 485 " pdb=" CA PRO B 485 " ideal model delta harmonic sigma weight residual 180.00 137.76 42.24 0 5.00e+00 4.00e-02 7.14e+01 dihedral pdb=" CA LEU A 484 " pdb=" C LEU A 484 " pdb=" N PRO A 485 " pdb=" CA PRO A 485 " ideal model delta harmonic sigma weight residual 180.00 137.79 42.21 0 5.00e+00 4.00e-02 7.13e+01 ... (remaining 5345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 1410 0.147 - 0.293: 16 0.293 - 0.440: 0 0.440 - 0.587: 0 0.587 - 0.733: 1 Chirality restraints: 1427 Sorted by residual: chirality pdb=" C25 RS4 B 701 " pdb=" C20 RS4 B 701 " pdb=" C28 RS4 B 701 " pdb=" O1 RS4 B 701 " both_signs ideal model delta sigma weight residual False -3.23 -2.49 -0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" C13 CLR A 701 " pdb=" C12 CLR A 701 " pdb=" C14 CLR A 701 " pdb=" C17 CLR A 701 " both_signs ideal model delta sigma weight residual False -2.93 -2.64 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" C13 CLR B 702 " pdb=" C12 CLR B 702 " pdb=" C14 CLR B 702 " pdb=" C17 CLR B 702 " both_signs ideal model delta sigma weight residual False -2.93 -2.65 -0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 1424 not shown) Planarity restraints: 1520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 484 " -0.056 5.00e-02 4.00e+02 8.39e-02 1.13e+01 pdb=" N PRO A 485 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 485 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 485 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 484 " -0.056 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO B 485 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO B 485 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 485 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 378 " -0.008 2.00e-02 2.50e+03 1.67e-02 2.80e+00 pdb=" C ARG A 378 " 0.029 2.00e-02 2.50e+03 pdb=" O ARG A 378 " -0.011 2.00e-02 2.50e+03 pdb=" N TRP A 379 " -0.010 2.00e-02 2.50e+03 ... (remaining 1517 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2362 2.78 - 3.31: 8178 3.31 - 3.84: 14737 3.84 - 4.37: 17184 4.37 - 4.90: 28896 Nonbonded interactions: 71357 Sorted by model distance: nonbonded pdb=" OH TYR B 494 " pdb=" O LYS B 500 " model vdw 2.251 2.440 nonbonded pdb=" OH TYR A 494 " pdb=" O LYS A 500 " model vdw 2.252 2.440 nonbonded pdb=" N ASN B 338 " pdb=" OD1 ASN B 338 " model vdw 2.267 2.520 nonbonded pdb=" N ASN A 338 " pdb=" OD1 ASN A 338 " model vdw 2.267 2.520 nonbonded pdb=" O LEU A 146 " pdb=" OG1 THR A 371 " model vdw 2.280 2.440 ... (remaining 71352 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' and resid 35 through 654) selection = (chain 'B' and resid 35 through 654) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 5794 2.51 5 N 1454 2.21 5 O 1589 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 2.390 Check model and map are aligned: 0.140 Convert atoms to be neutral: 0.080 Process input model: 26.400 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 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 : 0.031 1.474 9089 Z= 2.097 Angle : 1.401 56.692 12318 Z= 0.635 Chirality : 0.058 0.733 1427 Planarity : 0.006 0.084 1520 Dihedral : 16.309 86.651 3247 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer Outliers : 3.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: -5.74 (0.17), residues: 1116 helix: -4.22 (0.09), residues: 616 sheet: -1.30 (0.85), residues: 34 loop : -3.22 (0.25), residues: 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 325 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 9 residues processed: 339 average time/residue: 0.2153 time to fit residues: 98.1324 Evaluate side-chains 231 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 222 time to evaluate : 0.965 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0800 time to fit residues: 2.7479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 chunk 53 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 GLN A 283 HIS A 391 ASN A 437 GLN A 457 HIS A 583 HIS A 601 ASN ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN B 120 ASN B 244 GLN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 583 HIS B 601 ASN ** B 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.106 9089 Z= 0.404 Angle : 1.076 30.876 12318 Z= 0.502 Chirality : 0.047 0.283 1427 Planarity : 0.007 0.085 1520 Dihedral : 8.222 149.840 1229 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: -4.53 (0.19), residues: 1116 helix: -2.85 (0.15), residues: 604 sheet: -1.30 (0.76), residues: 34 loop : -3.25 (0.25), residues: 478 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 283 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 283 average time/residue: 0.1803 time to fit residues: 72.8010 Evaluate side-chains 220 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 1.034 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 20.0000 chunk 31 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 101 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN B 398 GLN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.106 9089 Z= 0.404 Angle : 1.076 30.876 12318 Z= 0.502 Chirality : 0.047 0.283 1427 Planarity : 0.007 0.085 1520 Dihedral : 8.215 149.361 1229 Min Nonbonded Distance : 1.114 Molprobity Statistics. All-atom Clashscore : 27.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: -4.53 (0.19), residues: 1116 helix: -2.85 (0.15), residues: 604 sheet: -1.30 (0.76), residues: 34 loop : -3.25 (0.25), residues: 478 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 269 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 269 average time/residue: 0.1779 time to fit residues: 69.2654 Evaluate side-chains 215 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 1.001 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 68 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 630 HIS B 68 ASN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.106 9089 Z= 0.404 Angle : 1.076 30.876 12318 Z= 0.502 Chirality : 0.047 0.283 1427 Planarity : 0.007 0.085 1520 Dihedral : 8.223 149.913 1229 Min Nonbonded Distance : 1.187 Molprobity Statistics. All-atom Clashscore : 26.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: -4.53 (0.19), residues: 1116 helix: -2.85 (0.15), residues: 604 sheet: -1.30 (0.76), residues: 34 loop : -3.25 (0.25), residues: 478 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 264 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 264 average time/residue: 0.1712 time to fit residues: 65.4017 Evaluate side-chains 216 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 1.039 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 55 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.106 9089 Z= 0.404 Angle : 1.076 30.876 12318 Z= 0.502 Chirality : 0.047 0.283 1427 Planarity : 0.007 0.085 1520 Dihedral : 8.223 149.913 1229 Min Nonbonded Distance : 1.187 Molprobity Statistics. All-atom Clashscore : 26.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: -4.53 (0.19), residues: 1116 helix: -2.85 (0.15), residues: 604 sheet: -1.30 (0.76), residues: 34 loop : -3.25 (0.25), residues: 478 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 265 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 265 average time/residue: 0.1699 time to fit residues: 65.6829 Evaluate side-chains 216 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 0.928 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 108 optimal weight: 0.0980 chunk 89 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 20.0000 chunk 104 optimal weight: 0.9980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.106 9089 Z= 0.404 Angle : 1.076 30.876 12318 Z= 0.502 Chirality : 0.047 0.283 1427 Planarity : 0.007 0.085 1520 Dihedral : 8.223 149.913 1229 Min Nonbonded Distance : 1.187 Molprobity Statistics. All-atom Clashscore : 26.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: -4.53 (0.19), residues: 1116 helix: -2.85 (0.15), residues: 604 sheet: -1.30 (0.76), residues: 34 loop : -3.25 (0.25), residues: 478 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 264 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 264 average time/residue: 0.1741 time to fit residues: 66.8442 Evaluate side-chains 216 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 1.094 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 10.0000 chunk 61 optimal weight: 20.0000 chunk 79 optimal weight: 30.0000 chunk 91 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 107 optimal weight: 20.0000 chunk 67 optimal weight: 0.9990 chunk 65 optimal weight: 8.9990 chunk 49 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.106 9089 Z= 0.404 Angle : 1.076 30.876 12318 Z= 0.502 Chirality : 0.047 0.283 1427 Planarity : 0.007 0.085 1520 Dihedral : 8.223 149.913 1229 Min Nonbonded Distance : 1.187 Molprobity Statistics. All-atom Clashscore : 26.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: -4.53 (0.19), residues: 1116 helix: -2.85 (0.15), residues: 604 sheet: -1.30 (0.76), residues: 34 loop : -3.25 (0.25), residues: 478 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 264 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 264 average time/residue: 0.1679 time to fit residues: 64.2571 Evaluate side-chains 216 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 1.032 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 10 optimal weight: 0.0020 chunk 84 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 103 optimal weight: 0.0270 overall best weight: 1.4052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.106 9089 Z= 0.404 Angle : 1.076 30.876 12318 Z= 0.502 Chirality : 0.047 0.283 1427 Planarity : 0.007 0.085 1520 Dihedral : 8.223 149.913 1229 Min Nonbonded Distance : 1.187 Molprobity Statistics. All-atom Clashscore : 26.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: -4.53 (0.19), residues: 1116 helix: -2.85 (0.15), residues: 604 sheet: -1.30 (0.76), residues: 34 loop : -3.25 (0.25), residues: 478 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 264 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 264 average time/residue: 0.1785 time to fit residues: 68.4705 Evaluate side-chains 216 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 1.008 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 66 optimal weight: 10.0000 chunk 106 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.106 9089 Z= 0.404 Angle : 1.076 30.876 12318 Z= 0.502 Chirality : 0.047 0.283 1427 Planarity : 0.007 0.085 1520 Dihedral : 8.223 149.913 1229 Min Nonbonded Distance : 1.187 Molprobity Statistics. All-atom Clashscore : 26.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: -4.53 (0.19), residues: 1116 helix: -2.85 (0.15), residues: 604 sheet: -1.30 (0.76), residues: 34 loop : -3.25 (0.25), residues: 478 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 264 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 264 average time/residue: 0.1729 time to fit residues: 66.2493 Evaluate side-chains 216 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 0.999 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 9 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.106 9089 Z= 0.404 Angle : 1.076 30.876 12318 Z= 0.502 Chirality : 0.047 0.283 1427 Planarity : 0.007 0.085 1520 Dihedral : 8.223 149.913 1229 Min Nonbonded Distance : 1.187 Molprobity Statistics. All-atom Clashscore : 26.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: -4.53 (0.19), residues: 1116 helix: -2.85 (0.15), residues: 604 sheet: -1.30 (0.76), residues: 34 loop : -3.25 (0.25), residues: 478 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 264 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 264 average time/residue: 0.1749 time to fit residues: 66.9301 Evaluate side-chains 216 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 1.039 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 30.0000 chunk 88 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 78 optimal weight: 20.0000 chunk 5 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 ASN ** 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 = 0.3870 r_free = 0.3870 target = 0.152039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.116801 restraints weight = 19910.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.119917 restraints weight = 11717.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.121884 restraints weight = 8128.261| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.106 9089 Z= 0.404 Angle : 1.076 30.876 12318 Z= 0.502 Chirality : 0.047 0.283 1427 Planarity : 0.007 0.085 1520 Dihedral : 8.223 149.913 1229 Min Nonbonded Distance : 1.187 Molprobity Statistics. All-atom Clashscore : 26.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: -4.53 (0.19), residues: 1116 helix: -2.85 (0.15), residues: 604 sheet: -1.30 (0.76), residues: 34 loop : -3.25 (0.25), residues: 478 =============================================================================== Job complete usr+sys time: 1813.91 seconds wall clock time: 33 minutes 49.73 seconds (2029.73 seconds total)