Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 03:07:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxi_21438/04_2023/6vxi_21438_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxi_21438/04_2023/6vxi_21438.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxi_21438/04_2023/6vxi_21438.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxi_21438/04_2023/6vxi_21438.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxi_21438/04_2023/6vxi_21438_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxi_21438/04_2023/6vxi_21438_updated.pdb" } resolution = 3.7 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= 0.015 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: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 5794 2.51 5 N 1456 2.21 5 O 1590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 96": "NH1" <-> "NH2" Residue "A GLU 138": "OE1" <-> "OE2" Residue "A ARG 147": "NH1" <-> "NH2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A ARG 160": "NH1" <-> "NH2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A GLU 285": "OE1" <-> "OE2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "A ARG 426": "NH1" <-> "NH2" Residue "A GLU 451": "OE1" <-> "OE2" Residue "A ARG 482": "NH1" <-> "NH2" Residue "A GLU 585": "OE1" <-> "OE2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B ARG 147": "NH1" <-> "NH2" Residue "B GLU 159": "OE1" <-> "OE2" Residue "B ARG 160": "NH1" <-> "NH2" Residue "B ARG 246": "NH1" <-> "NH2" Residue "B GLU 285": "OE1" <-> "OE2" Residue "B GLU 344": "OE1" <-> "OE2" Residue "B ARG 426": "NH1" <-> "NH2" Residue "B GLU 451": "OE1" <-> "OE2" Residue "B ARG 482": "NH1" <-> "NH2" Residue "B GLU 585": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 8898 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: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'CLR': 1, 'MIX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.53, per 1000 atoms: 0.62 Number of scatterers: 8898 At special positions: 0 Unit cell: (104.55, 75.03, 127.92, 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 1590 8.00 N 1456 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=2.06 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS B 603 " distance=2.04 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.06 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: 3.56 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: 50 helices and 6 sheets defined 49.8% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 86 through 93 removed outlier: 3.788A pdb=" N LEU A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 117 No H-bonds generated for 'chain 'A' and resid 115 through 117' Processing helix chain 'A' and resid 136 through 146 removed outlier: 4.103A pdb=" N SER A 143 " --> pdb=" O ASN A 139 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 163 removed outlier: 4.191A pdb=" N GLU A 159 " --> pdb=" O HIS A 155 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ARG A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN A 162 " --> pdb=" O ASN A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 188 through 198 removed outlier: 3.653A pdb=" N LYS A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER A 195 " --> pdb=" O ARG A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 233 removed outlier: 4.660A pdb=" N ASN A 222 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA A 223 " --> pdb=" O THR A 220 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL A 224 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 226 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A 228 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET A 231 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS A 233 " --> pdb=" O ARG A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 279 removed outlier: 4.152A pdb=" N GLU A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 4.731A 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 331 through 337 removed outlier: 4.539A pdb=" N ILE A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N TYR A 336 " --> pdb=" O LEU A 332 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 331 through 337' Processing helix chain 'A' and resid 342 through 352 removed outlier: 4.031A pdb=" N ALA A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 390 removed outlier: 3.599A pdb=" N LYS A 382 " --> pdb=" O ARG A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 412 Processing helix chain 'A' and resid 420 through 445 removed outlier: 4.335A pdb=" N ILE A 423 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N GLN A 424 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG A 426 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ALA A 427 " --> pdb=" O GLN A 424 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL A 429 " --> pdb=" O ARG A 426 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU A 430 " --> pdb=" O ALA A 427 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU A 433 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR A 434 " --> pdb=" O PHE A 431 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR A 435 " --> pdb=" O PHE A 432 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER A 440 " --> pdb=" O GLN A 437 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N SER A 441 " --> pdb=" O CYS A 438 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A 442 " --> pdb=" O PHE A 439 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER A 443 " --> pdb=" O SER A 440 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA A 444 " --> pdb=" O SER A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 461 Processing helix chain 'A' and resid 466 through 477 removed outlier: 3.520A pdb=" N SER A 476 " --> pdb=" O GLY A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 482 No H-bonds generated for 'chain 'A' and resid 479 through 482' Processing helix chain 'A' and resid 484 through 497 removed outlier: 5.028A pdb=" N PHE A 489 " --> pdb=" O PRO A 485 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE A 492 " --> pdb=" O ILE A 488 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 528 removed outlier: 3.642A pdb=" N THR A 512 " --> pdb=" O VAL A 508 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA A 528 " --> pdb=" O ALA A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 542 removed outlier: 3.935A pdb=" N MET A 541 " --> pdb=" O ALA A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 549 No H-bonds generated for 'chain 'A' and resid 546 through 549' Processing helix chain 'A' and resid 563 through 570 removed outlier: 3.933A pdb=" N TRP A 567 " --> pdb=" O SER A 563 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU A 568 " --> pdb=" O TRP A 564 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N GLN A 569 " --> pdb=" O LEU A 565 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N TYR A 570 " --> pdb=" O SER A 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 563 through 570' Processing helix chain 'A' and resid 573 through 583 Processing helix chain 'A' and resid 610 through 617 removed outlier: 3.510A pdb=" N LYS A 616 " --> pdb=" O GLU A 612 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN A 617 " --> pdb=" O TYR A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 649 removed outlier: 4.305A pdb=" N LYS A 628 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL A 631 " --> pdb=" O LYS A 628 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA A 634 " --> pdb=" O VAL A 631 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N CYS A 635 " --> pdb=" O ALA A 632 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A 638 " --> pdb=" O CYS A 635 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE A 639 " --> pdb=" O MET A 636 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR A 642 " --> pdb=" O ILE A 639 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ILE A 643 " --> pdb=" O PHE A 640 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR A 645 " --> pdb=" O THR A 642 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 648 " --> pdb=" O TYR A 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 93 removed outlier: 3.787A pdb=" N LEU B 90 " --> pdb=" O LYS B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 117 No H-bonds generated for 'chain 'B' and resid 115 through 117' Processing helix chain 'B' and resid 136 through 146 removed outlier: 4.103A pdb=" N SER B 143 " --> pdb=" O ASN B 139 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 146 " --> pdb=" O PHE B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 163 removed outlier: 4.191A pdb=" N GLU B 159 " --> pdb=" O HIS B 155 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ARG B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE B 161 " --> pdb=" O LYS B 157 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN B 162 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 188 through 198 removed outlier: 3.653A pdb=" N LYS B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER B 195 " --> pdb=" O ARG B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 233 removed outlier: 4.660A pdb=" N ASN B 222 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA B 223 " --> pdb=" O THR B 220 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL B 224 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU B 226 " --> pdb=" O ALA B 223 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU B 228 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET B 231 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS B 233 " --> pdb=" O ARG B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 279 removed outlier: 4.152A pdb=" N GLU B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 4.732A 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 331 through 337 removed outlier: 4.538A pdb=" N ILE B 335 " --> pdb=" O LYS B 331 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N TYR B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 331 through 337' Processing helix chain 'B' and resid 342 through 352 removed outlier: 4.031A pdb=" N ALA B 347 " --> pdb=" O LYS B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 390 removed outlier: 3.599A pdb=" N LYS B 382 " --> pdb=" O ARG B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 412 Processing helix chain 'B' and resid 420 through 445 removed outlier: 4.334A pdb=" N ILE B 423 " --> pdb=" O SER B 420 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N GLN B 424 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG B 426 " --> pdb=" O ILE B 423 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ALA B 427 " --> pdb=" O GLN B 424 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY B 428 " --> pdb=" O ASN B 425 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL B 429 " --> pdb=" O ARG B 426 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU B 430 " --> pdb=" O ALA B 427 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU B 433 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR B 434 " --> pdb=" O PHE B 431 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR B 435 " --> pdb=" O PHE B 432 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER B 440 " --> pdb=" O GLN B 437 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N SER B 441 " --> pdb=" O CYS B 438 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL B 442 " --> pdb=" O PHE B 439 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER B 443 " --> pdb=" O SER B 440 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA B 444 " --> pdb=" O SER B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 461 Processing helix chain 'B' and resid 466 through 477 removed outlier: 3.520A pdb=" N SER B 476 " --> pdb=" O GLY B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 482 No H-bonds generated for 'chain 'B' and resid 479 through 482' Processing helix chain 'B' and resid 484 through 497 removed outlier: 5.028A pdb=" N PHE B 489 " --> pdb=" O PRO B 485 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE B 492 " --> pdb=" O ILE B 488 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 528 removed outlier: 3.641A pdb=" N THR B 512 " --> pdb=" O VAL B 508 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA B 528 " --> pdb=" O ALA B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 542 removed outlier: 3.934A pdb=" N MET B 541 " --> pdb=" O ALA B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 549 No H-bonds generated for 'chain 'B' and resid 546 through 549' Processing helix chain 'B' and resid 563 through 570 removed outlier: 3.932A pdb=" N TRP B 567 " --> pdb=" O SER B 563 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU B 568 " --> pdb=" O TRP B 564 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N GLN B 569 " --> pdb=" O LEU B 565 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N TYR B 570 " --> pdb=" O SER B 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 563 through 570' Processing helix chain 'B' and resid 573 through 583 Processing helix chain 'B' and resid 610 through 617 removed outlier: 3.510A pdb=" N LYS B 616 " --> pdb=" O GLU B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 649 removed outlier: 4.305A pdb=" N LYS B 628 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL B 631 " --> pdb=" O LYS B 628 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA B 634 " --> pdb=" O VAL B 631 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N CYS B 635 " --> pdb=" O ALA B 632 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL B 638 " --> pdb=" O CYS B 635 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE B 639 " --> pdb=" O MET B 636 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR B 642 " --> pdb=" O ILE B 639 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE B 643 " --> pdb=" O PHE B 640 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR B 645 " --> pdb=" O THR B 642 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B 648 " --> pdb=" O TYR B 645 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 37 through 40 removed outlier: 3.533A pdb=" N ASP A 105 " --> pdb=" O HIS A 40 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 75 through 77 removed outlier: 6.370A pdb=" N ILE A 238 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N GLY A 122 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ASP A 210 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL A 124 " --> pdb=" O ASP A 210 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 256 through 260 removed outlier: 3.540A pdb=" N PHE A 266 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ALA A 260 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N LEU A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 37 through 40 removed outlier: 3.534A pdb=" N ASP B 105 " --> pdb=" O HIS B 40 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 75 through 77 removed outlier: 6.372A pdb=" N ILE B 238 " --> pdb=" O ASN B 76 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N GLY B 122 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ASP B 210 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL B 124 " --> pdb=" O ASP B 210 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 256 through 260 removed outlier: 3.540A pdb=" N PHE B 266 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ALA B 260 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LEU B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) 269 hydrogen bonds defined for protein. 633 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: 2.38 Time building geometry restraints manager: 3.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1384 1.29 - 1.42: 2375 1.42 - 1.55: 5230 1.55 - 1.68: 7 1.68 - 1.81: 94 Bond restraints: 9090 Sorted by residual: bond pdb=" CAY MIX B 701 " pdb=" NAU MIX B 701 " ideal model delta sigma weight residual 1.342 1.491 -0.149 2.00e-02 2.50e+03 5.58e+01 bond pdb=" CAZ MIX B 701 " pdb=" NAV MIX B 701 " ideal model delta sigma weight residual 1.343 1.465 -0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" CBA MIX B 701 " pdb=" CBE MIX B 701 " ideal model delta sigma weight residual 1.442 1.554 -0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" CBA MIX B 701 " pdb=" OAA MIX B 701 " ideal model delta sigma weight residual 1.254 1.156 0.098 2.00e-02 2.50e+03 2.43e+01 bond pdb=" CBB MIX B 701 " pdb=" CBD MIX B 701 " ideal model delta sigma weight residual 1.459 1.552 -0.093 2.00e-02 2.50e+03 2.18e+01 ... (remaining 9085 not shown) Histogram of bond angle deviations from ideal: 99.21 - 106.25: 195 106.25 - 113.29: 5017 113.29 - 120.33: 3755 120.33 - 127.37: 3267 127.37 - 134.41: 78 Bond angle restraints: 12312 Sorted by residual: angle pdb=" C ASP A 217 " pdb=" N SER A 218 " pdb=" CA SER A 218 " ideal model delta sigma weight residual 121.54 128.93 -7.39 1.91e+00 2.74e-01 1.50e+01 angle pdb=" C ASP B 217 " pdb=" N SER B 218 " pdb=" CA SER B 218 " ideal model delta sigma weight residual 121.54 128.90 -7.36 1.91e+00 2.74e-01 1.48e+01 angle pdb=" N SER A 218 " pdb=" CA SER A 218 " pdb=" C SER A 218 " ideal model delta sigma weight residual 110.80 118.07 -7.27 2.13e+00 2.20e-01 1.16e+01 angle pdb=" N SER B 218 " pdb=" CA SER B 218 " pdb=" C SER B 218 " ideal model delta sigma weight residual 110.80 118.05 -7.25 2.13e+00 2.20e-01 1.16e+01 angle pdb=" C ILE B 108 " pdb=" N ASN B 109 " pdb=" CA ASN B 109 " ideal model delta sigma weight residual 121.54 127.90 -6.36 1.91e+00 2.74e-01 1.11e+01 ... (remaining 12307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 4686 17.79 - 35.59: 505 35.59 - 53.38: 135 53.38 - 71.18: 18 71.18 - 88.97: 11 Dihedral angle restraints: 5355 sinusoidal: 2095 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 18.11 74.89 1 1.00e+01 1.00e-02 7.10e+01 dihedral pdb=" CB CYS A 592 " pdb=" SG CYS A 592 " pdb=" SG CYS A 608 " pdb=" CB CYS A 608 " ideal model delta sinusoidal sigma weight residual 93.00 40.22 52.78 1 1.00e+01 1.00e-02 3.79e+01 dihedral pdb=" CB CYS B 592 " pdb=" SG CYS B 592 " pdb=" SG CYS B 608 " pdb=" CB CYS B 608 " ideal model delta sinusoidal sigma weight residual 93.00 40.23 52.77 1 1.00e+01 1.00e-02 3.79e+01 ... (remaining 5352 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1043 0.057 - 0.114: 312 0.114 - 0.172: 57 0.172 - 0.229: 8 0.229 - 0.286: 6 Chirality restraints: 1426 Sorted by residual: 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 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 -2.65 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CB ILE B 487 " pdb=" CA ILE B 487 " pdb=" CG1 ILE B 487 " pdb=" CG2 ILE B 487 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 1423 not shown) Planarity restraints: 1519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 429 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.54e+00 pdb=" C VAL A 429 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL A 429 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU A 430 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 429 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.47e+00 pdb=" C VAL B 429 " -0.032 2.00e-02 2.50e+03 pdb=" O VAL B 429 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU B 430 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 622 " 0.029 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO A 623 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 623 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 623 " 0.024 5.00e-02 4.00e+02 ... (remaining 1516 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2715 2.81 - 3.33: 8209 3.33 - 3.85: 14459 3.85 - 4.38: 17279 4.38 - 4.90: 29255 Nonbonded interactions: 71917 Sorted by model distance: nonbonded pdb=" OG1 THR B 133 " pdb=" OD1 ASN B 387 " model vdw 2.281 2.440 nonbonded pdb=" OG1 THR A 133 " pdb=" OD1 ASN A 387 " model vdw 2.282 2.440 nonbonded pdb=" OH TYR B 494 " pdb=" O LYS B 500 " model vdw 2.297 2.440 nonbonded pdb=" OH TYR A 494 " pdb=" O LYS A 500 " model vdw 2.297 2.440 nonbonded pdb=" OD1 ASN B 436 " pdb=" OAD MIX B 701 " model vdw 2.306 2.440 ... (remaining 71912 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 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: 0.530 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: 2.360 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 26.700 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 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 : 0.008 0.149 9090 Z= 0.551 Angle : 0.998 11.139 12312 Z= 0.502 Chirality : 0.058 0.286 1426 Planarity : 0.005 0.043 1519 Dihedral : 15.999 88.972 3254 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.50 % Favored : 90.32 % Rotamer Outliers : 2.07 % 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: -6.00 (0.17), residues: 1116 helix: -4.44 (0.09), residues: 566 sheet: -4.21 (0.49), residues: 44 loop : -3.26 (0.24), residues: 506 *********************** 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 275 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 255 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 4 residues processed: 267 average time/residue: 0.2193 time to fit residues: 79.3653 Evaluate side-chains 176 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 172 time to evaluate : 1.040 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0825 time to fit residues: 2.0541 ------------------------------------------------------------------------------- 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: 2.9990 chunk 84 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS A 109 ASN A 158 ASN A 267 HIS A 393 GLN A 457 HIS A 583 HIS A 629 ASN B 40 HIS B 109 ASN B 158 ASN B 267 HIS B 393 GLN B 457 HIS B 583 HIS B 629 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 9090 Z= 0.310 Angle : 0.725 10.573 12312 Z= 0.365 Chirality : 0.043 0.163 1426 Planarity : 0.005 0.031 1519 Dihedral : 6.151 49.554 1236 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.53 % Favored : 92.29 % Rotamer Outliers : 3.01 % 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: -4.41 (0.20), residues: 1116 helix: -2.71 (0.17), residues: 554 sheet: -4.22 (0.48), residues: 48 loop : -2.98 (0.24), residues: 514 *********************** 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 225 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 196 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 18 residues processed: 213 average time/residue: 0.1796 time to fit residues: 55.2641 Evaluate side-chains 190 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 172 time to evaluate : 1.068 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.0853 time to fit residues: 4.3046 ------------------------------------------------------------------------------- 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: 10.0000 chunk 31 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 69 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 81 optimal weight: 30.0000 chunk 100 optimal weight: 0.0040 overall best weight: 1.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 GLN ** B 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 9090 Z= 0.234 Angle : 0.641 10.119 12312 Z= 0.319 Chirality : 0.042 0.192 1426 Planarity : 0.004 0.036 1519 Dihedral : 5.747 45.708 1236 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.97 % Favored : 91.85 % Rotamer Outliers : 3.11 % 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: -3.62 (0.22), residues: 1116 helix: -1.87 (0.20), residues: 564 sheet: -3.91 (0.52), residues: 48 loop : -2.83 (0.26), residues: 504 *********************** 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 225 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 195 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 16 residues processed: 214 average time/residue: 0.1789 time to fit residues: 56.0770 Evaluate side-chains 190 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 174 time to evaluate : 1.094 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0949 time to fit residues: 4.2835 ------------------------------------------------------------------------------- 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: 9.9990 chunk 52 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 48 optimal weight: 0.0070 chunk 68 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 299 ASN B 299 ASN B 391 ASN B 425 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 9090 Z= 0.224 Angle : 0.629 11.419 12312 Z= 0.311 Chirality : 0.042 0.181 1426 Planarity : 0.003 0.031 1519 Dihedral : 5.438 40.391 1236 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.24 % Favored : 91.58 % Rotamer Outliers : 2.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.23), residues: 1116 helix: -1.42 (0.21), residues: 562 sheet: -3.56 (0.57), residues: 44 loop : -2.80 (0.26), residues: 510 *********************** 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 224 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 196 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 10 residues processed: 211 average time/residue: 0.1716 time to fit residues: 53.7998 Evaluate side-chains 195 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 185 time to evaluate : 1.108 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0923 time to fit residues: 3.1298 ------------------------------------------------------------------------------- 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: 0.3980 chunk 1 optimal weight: 8.9990 chunk 80 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 92 optimal weight: 0.7980 chunk 74 optimal weight: 0.3980 chunk 0 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 9090 Z= 0.187 Angle : 0.619 10.765 12312 Z= 0.302 Chirality : 0.041 0.167 1426 Planarity : 0.003 0.040 1519 Dihedral : 5.283 40.307 1236 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.17 % Favored : 92.65 % Rotamer Outliers : 1.66 % 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: -2.98 (0.24), residues: 1116 helix: -1.18 (0.22), residues: 558 sheet: -3.47 (0.54), residues: 48 loop : -2.74 (0.26), residues: 510 *********************** 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 213 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 197 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 5 residues processed: 208 average time/residue: 0.1671 time to fit residues: 52.2850 Evaluate side-chains 190 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 185 time to evaluate : 1.199 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0992 time to fit residues: 2.4671 ------------------------------------------------------------------------------- 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: 0.9990 chunk 21 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 26 optimal weight: 0.0970 chunk 108 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 104 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 9090 Z= 0.169 Angle : 0.613 10.225 12312 Z= 0.298 Chirality : 0.041 0.173 1426 Planarity : 0.003 0.042 1519 Dihedral : 5.132 39.953 1236 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.62 % Favored : 92.29 % Rotamer Outliers : 2.18 % 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: -2.78 (0.24), residues: 1116 helix: -1.03 (0.22), residues: 554 sheet: -2.93 (0.63), residues: 44 loop : -2.67 (0.26), residues: 518 *********************** 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 226 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 205 time to evaluate : 1.048 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 13 residues processed: 216 average time/residue: 0.1713 time to fit residues: 54.8771 Evaluate side-chains 201 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 188 time to evaluate : 1.121 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0916 time to fit residues: 3.5834 ------------------------------------------------------------------------------- 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: 9.9990 chunk 61 optimal weight: 5.9990 chunk 79 optimal weight: 20.0000 chunk 91 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 9090 Z= 0.323 Angle : 0.715 9.452 12312 Z= 0.354 Chirality : 0.045 0.175 1426 Planarity : 0.004 0.042 1519 Dihedral : 5.363 41.046 1236 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.14 % Favored : 90.77 % Rotamer Outliers : 2.07 % 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: -2.65 (0.24), residues: 1116 helix: -0.99 (0.21), residues: 564 sheet: -3.10 (0.59), residues: 48 loop : -2.51 (0.27), residues: 504 *********************** 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 210 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 190 time to evaluate : 1.123 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 204 average time/residue: 0.1725 time to fit residues: 52.3453 Evaluate side-chains 194 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 183 time to evaluate : 1.108 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0908 time to fit residues: 3.3319 ------------------------------------------------------------------------------- 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: 7.9990 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 84 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.078 9090 Z= 0.266 Angle : 0.690 9.922 12312 Z= 0.335 Chirality : 0.044 0.183 1426 Planarity : 0.004 0.040 1519 Dihedral : 5.368 40.782 1236 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.69 % Favored : 91.22 % Rotamer Outliers : 1.35 % 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: -2.61 (0.25), residues: 1116 helix: -0.98 (0.22), residues: 566 sheet: -2.99 (0.59), residues: 48 loop : -2.48 (0.27), residues: 502 *********************** 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 206 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 193 time to evaluate : 1.089 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 199 average time/residue: 0.1747 time to fit residues: 51.8564 Evaluate side-chains 189 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 179 time to evaluate : 1.065 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0868 time to fit residues: 3.1120 ------------------------------------------------------------------------------- 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: 3.9990 chunk 100 optimal weight: 20.0000 chunk 103 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 106 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.094 9090 Z= 0.370 Angle : 0.758 10.144 12312 Z= 0.373 Chirality : 0.046 0.179 1426 Planarity : 0.004 0.038 1519 Dihedral : 5.553 40.998 1236 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.32 % Favored : 90.50 % Rotamer Outliers : 0.83 % 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: -2.66 (0.25), residues: 1116 helix: -1.08 (0.21), residues: 572 sheet: -3.17 (0.59), residues: 48 loop : -2.41 (0.28), residues: 496 *********************** 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 197 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 189 time to evaluate : 1.111 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 191 average time/residue: 0.1744 time to fit residues: 49.5675 Evaluate side-chains 189 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 182 time to evaluate : 1.132 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0895 time to fit residues: 2.7442 ------------------------------------------------------------------------------- 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: 0.0980 chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 111 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 88 optimal weight: 0.0970 chunk 9 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 590 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 9090 Z= 0.172 Angle : 0.660 10.535 12312 Z= 0.317 Chirality : 0.042 0.194 1426 Planarity : 0.003 0.038 1519 Dihedral : 5.133 39.838 1236 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer Outliers : 0.41 % 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: -2.44 (0.25), residues: 1116 helix: -0.92 (0.22), residues: 560 sheet: -2.54 (0.66), residues: 44 loop : -2.32 (0.28), residues: 512 ********************** 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 201 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 197 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 200 average time/residue: 0.1778 time to fit residues: 52.6274 Evaluate side-chains 196 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 193 time to evaluate : 1.095 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0900 time to fit residues: 1.9492 ------------------------------------------------------------------------------- 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: 0.9990 chunk 81 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.0570 chunk 78 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.157131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.125001 restraints weight = 13623.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.126017 restraints weight = 8913.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.126483 restraints weight = 6311.973| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.072 9090 Z= 0.332 Angle : 0.733 10.564 12312 Z= 0.356 Chirality : 0.045 0.180 1426 Planarity : 0.004 0.039 1519 Dihedral : 5.334 40.525 1236 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.86 % Favored : 90.05 % Rotamer Outliers : 0.52 % 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: -2.53 (0.25), residues: 1116 helix: -1.02 (0.22), residues: 568 sheet: -2.92 (0.59), residues: 48 loop : -2.29 (0.28), residues: 500 =============================================================================== Job complete usr+sys time: 1818.73 seconds wall clock time: 34 minutes 1.22 seconds (2041.22 seconds total)