Starting phenix.real_space_refine on Thu Feb 15 10:28:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l3h_0822/02_2024/6l3h_0822_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l3h_0822/02_2024/6l3h_0822.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l3h_0822/02_2024/6l3h_0822.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l3h_0822/02_2024/6l3h_0822.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l3h_0822/02_2024/6l3h_0822_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l3h_0822/02_2024/6l3h_0822_updated.pdb" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 6 7.16 5 S 50 5.16 5 C 7950 2.51 5 N 1902 2.21 5 O 2056 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 52": "OD1" <-> "OD2" Residue "A ASP 53": "OD1" <-> "OD2" Residue "A ARG 90": "NH1" <-> "NH2" Residue "A ASP 97": "OD1" <-> "OD2" Residue "A GLU 110": "OE1" <-> "OE2" Residue "A GLU 114": "OE1" <-> "OE2" Residue "A ASP 143": "OD1" <-> "OD2" Residue "A ASP 162": "OD1" <-> "OD2" Residue "A ASP 163": "OD1" <-> "OD2" Residue "A GLU 171": "OE1" <-> "OE2" Residue "A GLU 184": "OE1" <-> "OE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A GLU 265": "OE1" <-> "OE2" Residue "A PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 414": "OD1" <-> "OD2" Residue "A GLU 573": "OE1" <-> "OE2" Residue "A GLU 576": "OE1" <-> "OE2" Residue "A GLU 585": "OE1" <-> "OE2" Residue "A ARG 591": "NH1" <-> "NH2" Residue "B ASP 52": "OD1" <-> "OD2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B ARG 90": "NH1" <-> "NH2" Residue "B ASP 97": "OD1" <-> "OD2" Residue "B GLU 110": "OE1" <-> "OE2" Residue "B GLU 114": "OE1" <-> "OE2" Residue "B ASP 143": "OD1" <-> "OD2" Residue "B ASP 162": "OD1" <-> "OD2" Residue "B ASP 163": "OD1" <-> "OD2" Residue "B GLU 171": "OE1" <-> "OE2" Residue "B GLU 184": "OE1" <-> "OE2" Residue "B GLU 265": "OE1" <-> "OE2" Residue "B PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 414": "OD1" <-> "OD2" Residue "B GLU 573": "OE1" <-> "OE2" Residue "B GLU 576": "OE1" <-> "OE2" Residue "B GLU 585": "OE1" <-> "OE2" Residue "B ARG 591": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11966 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5895 Classifications: {'peptide': 741} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 711} Chain breaks: 1 Chain: "B" Number of atoms: 5895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5895 Classifications: {'peptide': 741} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 711} Chain breaks: 1 Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Unusual residues: {' CA': 1, ' FE': 1, 'HEM': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Unusual residues: {' CA': 1, ' FE': 1, 'HEM': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 6.58, per 1000 atoms: 0.55 Number of scatterers: 11966 At special positions: 0 Unit cell: (75.97, 114.49, 107, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 6 26.01 Ca 2 19.99 S 50 16.00 O 2056 8.00 N 1902 7.00 C 7950 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.63 Conformation dependent library (CDL) restraints added in 2.2 seconds 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2712 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 70 helices and 2 sheets defined 61.5% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.60 Creating SS restraints... Processing helix chain 'A' and resid 5 through 24 removed outlier: 3.582A pdb=" N VAL A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR A 20 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 32 No H-bonds generated for 'chain 'A' and resid 29 through 32' Processing helix chain 'A' and resid 51 through 64 removed outlier: 3.532A pdb=" N GLN A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR A 63 " --> pdb=" O SER A 59 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR A 64 " --> pdb=" O ALA A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 68 No H-bonds generated for 'chain 'A' and resid 66 through 68' Processing helix chain 'A' and resid 83 through 99 removed outlier: 3.552A pdb=" N HIS A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 126 removed outlier: 4.313A pdb=" N ASP A 125 " --> pdb=" O THR A 121 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU A 126 " --> pdb=" O ARG A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 160 removed outlier: 3.511A pdb=" N LYS A 147 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 153 " --> pdb=" O ILE A 149 " (cutoff:3.500A) Proline residue: A 154 - end of helix Processing helix chain 'A' and resid 183 through 186 No H-bonds generated for 'chain 'A' and resid 183 through 186' Processing helix chain 'A' and resid 188 through 199 removed outlier: 3.527A pdb=" N PHE A 192 " --> pdb=" O LYS A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 221 No H-bonds generated for 'chain 'A' and resid 219 through 221' Processing helix chain 'A' and resid 227 through 253 removed outlier: 3.705A pdb=" N SER A 233 " --> pdb=" O ASN A 229 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A 236 " --> pdb=" O TRP A 232 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL A 237 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL A 238 " --> pdb=" O PHE A 234 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 287 removed outlier: 3.887A pdb=" N GLY A 281 " --> pdb=" O LYS A 278 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS A 282 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 284 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE A 285 " --> pdb=" O LYS A 282 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 286 " --> pdb=" O TYR A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 301 Processing helix chain 'A' and resid 322 through 325 No H-bonds generated for 'chain 'A' and resid 322 through 325' Processing helix chain 'A' and resid 328 through 358 removed outlier: 4.097A pdb=" N ALA A 339 " --> pdb=" O HIS A 335 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Proline residue: A 356 - end of helix Processing helix chain 'A' and resid 367 through 393 removed outlier: 3.538A pdb=" N LEU A 393 " --> pdb=" O ASN A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 405 removed outlier: 4.590A pdb=" N PHE A 403 " --> pdb=" O GLU A 400 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TRP A 404 " --> pdb=" O PHE A 401 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE A 405 " --> pdb=" O ASN A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 442 removed outlier: 3.997A pdb=" N THR A 438 " --> pdb=" O MET A 434 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL A 439 " --> pdb=" O LEU A 435 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N SER A 440 " --> pdb=" O ARG A 436 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ALA A 441 " --> pdb=" O CYS A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 464 removed outlier: 3.719A pdb=" N PHE A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 463 " --> pdb=" O MET A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 469 No H-bonds generated for 'chain 'A' and resid 467 through 469' Processing helix chain 'A' and resid 478 through 484 removed outlier: 3.709A pdb=" N TYR A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 511 removed outlier: 4.291A pdb=" N THR A 502 " --> pdb=" O GLU A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 533 removed outlier: 3.525A pdb=" N THR A 521 " --> pdb=" O ARG A 517 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A 525 " --> pdb=" O THR A 521 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA A 529 " --> pdb=" O LEU A 525 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE A 530 " --> pdb=" O ALA A 526 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N MET A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 542 Processing helix chain 'A' and resid 552 through 559 removed outlier: 3.930A pdb=" N ALA A 557 " --> pdb=" O MET A 553 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N CYS A 558 " --> pdb=" O ALA A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 568 No H-bonds generated for 'chain 'A' and resid 565 through 568' Processing helix chain 'A' and resid 571 through 583 removed outlier: 3.695A pdb=" N TYR A 575 " --> pdb=" O GLY A 571 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU A 576 " --> pdb=" O ARG A 572 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLN A 581 " --> pdb=" O HIS A 577 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N HIS A 582 " --> pdb=" O TRP A 578 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU A 583 " --> pdb=" O SER A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 606 removed outlier: 3.508A pdb=" N ALA A 601 " --> pdb=" O PHE A 597 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET A 605 " --> pdb=" O ALA A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 624 removed outlier: 4.190A pdb=" N TYR A 623 " --> pdb=" O ILE A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 654 removed outlier: 4.516A pdb=" N PHE A 644 " --> pdb=" O GLY A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 684 removed outlier: 3.805A pdb=" N TRP A 670 " --> pdb=" O LYS A 666 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TRP A 673 " --> pdb=" O THR A 669 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A 680 " --> pdb=" O ASN A 676 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE A 683 " --> pdb=" O LEU A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 700 removed outlier: 3.618A pdb=" N ALA A 697 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER A 698 " --> pdb=" O GLN A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 706 No H-bonds generated for 'chain 'A' and resid 703 through 706' Processing helix chain 'A' and resid 709 through 712 No H-bonds generated for 'chain 'A' and resid 709 through 712' Processing helix chain 'A' and resid 723 through 745 removed outlier: 4.540A pdb=" N LEU A 729 " --> pdb=" O ALA A 726 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE A 730 " --> pdb=" O ALA A 727 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE A 745 " --> pdb=" O ALA A 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 24 removed outlier: 3.583A pdb=" N VAL B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 32 No H-bonds generated for 'chain 'B' and resid 29 through 32' Processing helix chain 'B' and resid 51 through 64 removed outlier: 3.533A pdb=" N GLN B 62 " --> pdb=" O GLN B 58 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR B 63 " --> pdb=" O SER B 59 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR B 64 " --> pdb=" O ALA B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 68 No H-bonds generated for 'chain 'B' and resid 66 through 68' Processing helix chain 'B' and resid 83 through 99 removed outlier: 3.552A pdb=" N HIS B 89 " --> pdb=" O ALA B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 126 removed outlier: 4.314A pdb=" N ASP B 125 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU B 126 " --> pdb=" O ARG B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 160 removed outlier: 3.509A pdb=" N LYS B 147 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE B 152 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B 153 " --> pdb=" O ILE B 149 " (cutoff:3.500A) Proline residue: B 154 - end of helix Processing helix chain 'B' and resid 183 through 186 No H-bonds generated for 'chain 'B' and resid 183 through 186' Processing helix chain 'B' and resid 188 through 199 removed outlier: 3.525A pdb=" N PHE B 192 " --> pdb=" O LYS B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 221 No H-bonds generated for 'chain 'B' and resid 219 through 221' Processing helix chain 'B' and resid 227 through 253 removed outlier: 3.706A pdb=" N SER B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER B 236 " --> pdb=" O TRP B 232 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL B 237 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL B 238 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY B 245 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 287 removed outlier: 3.887A pdb=" N GLY B 281 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS B 282 " --> pdb=" O ALA B 279 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL B 284 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE B 285 " --> pdb=" O LYS B 282 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU B 286 " --> pdb=" O TYR B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 301 Processing helix chain 'B' and resid 322 through 325 No H-bonds generated for 'chain 'B' and resid 322 through 325' Processing helix chain 'B' and resid 328 through 358 removed outlier: 4.098A pdb=" N ALA B 339 " --> pdb=" O HIS B 335 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE B 340 " --> pdb=" O ILE B 336 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) Proline residue: B 356 - end of helix Processing helix chain 'B' and resid 367 through 393 removed outlier: 3.538A pdb=" N LEU B 393 " --> pdb=" O ASN B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 405 removed outlier: 4.591A pdb=" N PHE B 403 " --> pdb=" O GLU B 400 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TRP B 404 " --> pdb=" O PHE B 401 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE B 405 " --> pdb=" O ASN B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 442 removed outlier: 3.997A pdb=" N THR B 438 " --> pdb=" O MET B 434 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL B 439 " --> pdb=" O LEU B 435 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N SER B 440 " --> pdb=" O ARG B 436 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ALA B 441 " --> pdb=" O CYS B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.720A pdb=" N PHE B 455 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY B 463 " --> pdb=" O MET B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 469 No H-bonds generated for 'chain 'B' and resid 467 through 469' Processing helix chain 'B' and resid 478 through 484 removed outlier: 3.709A pdb=" N TYR B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 511 removed outlier: 4.291A pdb=" N THR B 502 " --> pdb=" O GLU B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 533 removed outlier: 3.525A pdb=" N THR B 521 " --> pdb=" O ARG B 517 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU B 525 " --> pdb=" O THR B 521 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA B 529 " --> pdb=" O LEU B 525 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE B 530 " --> pdb=" O ALA B 526 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N MET B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 552 through 559 removed outlier: 3.930A pdb=" N ALA B 557 " --> pdb=" O MET B 553 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N CYS B 558 " --> pdb=" O ALA B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 568 No H-bonds generated for 'chain 'B' and resid 565 through 568' Processing helix chain 'B' and resid 571 through 583 removed outlier: 3.694A pdb=" N TYR B 575 " --> pdb=" O GLY B 571 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU B 576 " --> pdb=" O ARG B 572 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLN B 581 " --> pdb=" O HIS B 577 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N HIS B 582 " --> pdb=" O TRP B 578 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU B 583 " --> pdb=" O SER B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 606 removed outlier: 3.507A pdb=" N ALA B 601 " --> pdb=" O PHE B 597 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET B 605 " --> pdb=" O ALA B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 624 removed outlier: 4.189A pdb=" N TYR B 623 " --> pdb=" O ILE B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 654 removed outlier: 4.516A pdb=" N PHE B 644 " --> pdb=" O GLY B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 684 removed outlier: 3.805A pdb=" N TRP B 670 " --> pdb=" O LYS B 666 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TRP B 673 " --> pdb=" O THR B 669 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL B 680 " --> pdb=" O ASN B 676 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE B 683 " --> pdb=" O LEU B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 700 removed outlier: 3.618A pdb=" N ALA B 697 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B 698 " --> pdb=" O GLN B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 706 No H-bonds generated for 'chain 'B' and resid 703 through 706' Processing helix chain 'B' and resid 709 through 712 No H-bonds generated for 'chain 'B' and resid 709 through 712' Processing helix chain 'B' and resid 723 through 745 removed outlier: 4.540A pdb=" N LEU B 729 " --> pdb=" O ALA B 726 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ILE B 730 " --> pdb=" O ALA B 727 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE B 745 " --> pdb=" O ALA B 742 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 39 through 42 Processing sheet with id= B, first strand: chain 'B' and resid 39 through 42 512 hydrogen bonds defined for protein. 1392 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: 3.29 Time building geometry restraints manager: 5.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.37: 4553 1.37 - 1.54: 7683 1.54 - 1.71: 26 1.71 - 1.88: 90 1.88 - 2.05: 16 Bond restraints: 12368 Sorted by residual: bond pdb=" C ARG A 368 " pdb=" O ARG A 368 " ideal model delta sigma weight residual 1.236 1.204 0.032 1.25e-02 6.40e+03 6.68e+00 bond pdb=" N LYS A 365 " pdb=" CA LYS A 365 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.24e+00 bond pdb=" N SER B 44 " pdb=" CA SER B 44 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.19e-02 7.06e+03 5.75e+00 bond pdb=" N TRP A 722 " pdb=" CA TRP A 722 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.27e-02 6.20e+03 5.69e+00 bond pdb=" N LYS B 365 " pdb=" CA LYS B 365 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.66e+00 ... (remaining 12363 not shown) Histogram of bond angle deviations from ideal: 87.35 - 105.12: 217 105.12 - 122.89: 15803 122.89 - 140.66: 888 140.66 - 158.43: 0 158.43 - 176.20: 8 Bond angle restraints: 16916 Sorted by residual: angle pdb=" N TRP A 722 " pdb=" CA TRP A 722 " pdb=" C TRP A 722 " ideal model delta sigma weight residual 113.41 107.56 5.85 1.22e+00 6.72e-01 2.30e+01 angle pdb=" N TRP B 722 " pdb=" CA TRP B 722 " pdb=" C TRP B 722 " ideal model delta sigma weight residual 113.41 107.58 5.83 1.22e+00 6.72e-01 2.28e+01 angle pdb=" N ILE B 606 " pdb=" CA ILE B 606 " pdb=" C ILE B 606 " ideal model delta sigma weight residual 112.96 108.23 4.73 1.00e+00 1.00e+00 2.24e+01 angle pdb=" N ILE A 606 " pdb=" CA ILE A 606 " pdb=" C ILE A 606 " ideal model delta sigma weight residual 112.96 108.24 4.72 1.00e+00 1.00e+00 2.23e+01 angle pdb=" N VAL A 723 " pdb=" CA VAL A 723 " pdb=" C VAL A 723 " ideal model delta sigma weight residual 113.07 107.75 5.32 1.36e+00 5.41e-01 1.53e+01 ... (remaining 16911 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.26: 6199 17.26 - 34.52: 558 34.52 - 51.79: 87 51.79 - 69.05: 24 69.05 - 86.31: 10 Dihedral angle restraints: 6878 sinusoidal: 2622 harmonic: 4256 Sorted by residual: dihedral pdb=" CA PHE B 471 " pdb=" C PHE B 471 " pdb=" N TYR B 472 " pdb=" CA TYR B 472 " ideal model delta harmonic sigma weight residual 180.00 147.83 32.17 0 5.00e+00 4.00e-02 4.14e+01 dihedral pdb=" CA PHE A 471 " pdb=" C PHE A 471 " pdb=" N TYR A 472 " pdb=" CA TYR A 472 " ideal model delta harmonic sigma weight residual 180.00 147.86 32.14 0 5.00e+00 4.00e-02 4.13e+01 dihedral pdb=" CA GLU B 265 " pdb=" C GLU B 265 " pdb=" N ASP B 266 " pdb=" CA ASP B 266 " ideal model delta harmonic sigma weight residual 180.00 152.62 27.38 0 5.00e+00 4.00e-02 3.00e+01 ... (remaining 6875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1071 0.038 - 0.077: 575 0.077 - 0.115: 142 0.115 - 0.154: 16 0.154 - 0.192: 4 Chirality restraints: 1808 Sorted by residual: chirality pdb=" CA TRP B 722 " pdb=" N TRP B 722 " pdb=" C TRP B 722 " pdb=" CB TRP B 722 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.24e-01 chirality pdb=" CA TRP A 722 " pdb=" N TRP A 722 " pdb=" C TRP A 722 " pdb=" CB TRP A 722 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.12e-01 chirality pdb=" CA PHE A 471 " pdb=" N PHE A 471 " pdb=" C PHE A 471 " pdb=" CB PHE A 471 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.54e-01 ... (remaining 1805 not shown) Planarity restraints: 2080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 471 " -0.023 2.00e-02 2.50e+03 1.71e-02 5.11e+00 pdb=" CG PHE A 471 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE A 471 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 471 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 471 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 471 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 471 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 471 " 0.023 2.00e-02 2.50e+03 1.70e-02 5.06e+00 pdb=" CG PHE B 471 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE B 471 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE B 471 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 471 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 471 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 471 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 153 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.53e+00 pdb=" N PRO B 154 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 154 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 154 " -0.026 5.00e-02 4.00e+02 ... (remaining 2077 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 80 2.61 - 3.18: 10510 3.18 - 3.75: 17639 3.75 - 4.33: 27550 4.33 - 4.90: 44377 Nonbonded interactions: 100156 Sorted by model distance: nonbonded pdb=" ND1 HIS B 490 " pdb="FE FE B 803 " model vdw 2.036 2.340 nonbonded pdb=" ND1 HIS A 490 " pdb="FE FE A 803 " model vdw 2.036 2.340 nonbonded pdb=" OG SER A 338 " pdb=" OH TYR A 386 " model vdw 2.094 2.440 nonbonded pdb=" OG SER B 338 " pdb=" OH TYR B 386 " model vdw 2.096 2.440 nonbonded pdb=" OE1 GLU B 494 " pdb="FE FE B 803 " model vdw 2.157 2.260 ... (remaining 100151 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 individual isotropic 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: 0.340 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: 2.490 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 33.860 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 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 : 0.007 0.070 12368 Z= 0.467 Angle : 0.767 14.073 16916 Z= 0.412 Chirality : 0.047 0.192 1808 Planarity : 0.004 0.047 2080 Dihedral : 13.750 86.311 4166 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.16 % Allowed : 3.13 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -4.60 (0.18), residues: 1474 helix: -2.86 (0.13), residues: 978 sheet: None (None), residues: 0 loop : -3.08 (0.24), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 342 HIS 0.008 0.001 HIS B 157 PHE 0.038 0.002 PHE A 471 TYR 0.015 0.002 TYR A 328 ARG 0.002 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 119 time to evaluate : 1.427 Fit side-chains REVERT: A 365 LYS cc_start: 0.5545 (mttt) cc_final: 0.5007 (mptt) REVERT: A 682 MET cc_start: 0.8798 (ptt) cc_final: 0.8446 (ptt) REVERT: B 365 LYS cc_start: 0.5827 (mttt) cc_final: 0.5487 (mtpt) REVERT: B 682 MET cc_start: 0.8774 (ptt) cc_final: 0.8402 (ptt) REVERT: B 728 ASP cc_start: 0.7381 (m-30) cc_final: 0.7131 (m-30) outliers start: 2 outliers final: 2 residues processed: 119 average time/residue: 0.3013 time to fit residues: 50.4324 Evaluate side-chains 90 residues out of total 1214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 88 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 722 TRP Chi-restraints excluded: chain B residue 722 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 134 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 277 GLN A 616 ASN A 741 GLN B 277 GLN B 741 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12368 Z= 0.194 Angle : 0.569 7.872 16916 Z= 0.292 Chirality : 0.040 0.152 1808 Planarity : 0.005 0.048 2080 Dihedral : 7.334 71.908 1624 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.32 % Allowed : 7.83 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -3.14 (0.19), residues: 1474 helix: -1.62 (0.15), residues: 968 sheet: None (None), residues: 0 loop : -2.78 (0.23), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 342 HIS 0.005 0.001 HIS A 542 PHE 0.022 0.001 PHE A 471 TYR 0.016 0.001 TYR B 472 ARG 0.003 0.000 ARG A 516 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 106 time to evaluate : 1.219 Fit side-chains REVERT: A 516 ARG cc_start: 0.8263 (tpp80) cc_final: 0.8006 (tpp80) REVERT: B 516 ARG cc_start: 0.8245 (tpp80) cc_final: 0.7992 (tpp80) outliers start: 16 outliers final: 10 residues processed: 115 average time/residue: 0.2496 time to fit residues: 41.9864 Evaluate side-chains 100 residues out of total 1214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 90 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 722 TRP Chi-restraints excluded: chain B residue 4 TYR Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 722 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 91 optimal weight: 0.4980 chunk 37 optimal weight: 3.9990 chunk 134 optimal weight: 8.9990 chunk 145 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 108 optimal weight: 8.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 277 GLN B 277 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12368 Z= 0.164 Angle : 0.532 8.532 16916 Z= 0.266 Chirality : 0.039 0.140 1808 Planarity : 0.004 0.043 2080 Dihedral : 7.024 72.828 1624 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.07 % Allowed : 9.47 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -2.08 (0.21), residues: 1474 helix: -0.76 (0.16), residues: 970 sheet: None (None), residues: 0 loop : -2.48 (0.24), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 342 HIS 0.005 0.001 HIS B 541 PHE 0.020 0.001 PHE A 471 TYR 0.013 0.001 TYR A 472 ARG 0.002 0.000 ARG A 516 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 95 time to evaluate : 1.334 Fit side-chains REVERT: A 516 ARG cc_start: 0.8314 (tpp80) cc_final: 0.8045 (tpp80) REVERT: B 516 ARG cc_start: 0.8274 (tpp80) cc_final: 0.8026 (tpp80) outliers start: 13 outliers final: 7 residues processed: 104 average time/residue: 0.2399 time to fit residues: 37.3868 Evaluate side-chains 98 residues out of total 1214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 91 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain B residue 4 TYR Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 228 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 64 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 135 optimal weight: 0.2980 chunk 143 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN B 277 GLN B 616 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12368 Z= 0.164 Angle : 0.515 8.924 16916 Z= 0.258 Chirality : 0.039 0.139 1808 Planarity : 0.004 0.039 2080 Dihedral : 6.555 72.659 1620 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.57 % Allowed : 9.80 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.21), residues: 1474 helix: -0.38 (0.17), residues: 982 sheet: None (None), residues: 0 loop : -2.39 (0.24), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 342 HIS 0.006 0.001 HIS B 541 PHE 0.020 0.001 PHE B 471 TYR 0.012 0.001 TYR A 472 ARG 0.002 0.000 ARG A 516 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 94 time to evaluate : 1.401 Fit side-chains REVERT: A 471 PHE cc_start: 0.7810 (OUTLIER) cc_final: 0.7536 (p90) REVERT: B 471 PHE cc_start: 0.7793 (OUTLIER) cc_final: 0.7514 (p90) outliers start: 19 outliers final: 14 residues processed: 106 average time/residue: 0.2289 time to fit residues: 36.8441 Evaluate side-chains 107 residues out of total 1214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 91 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 605 MET Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain B residue 4 TYR Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 471 PHE Chi-restraints excluded: chain B residue 605 MET Chi-restraints excluded: chain B residue 665 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 106 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 chunk 128 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN B 277 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12368 Z= 0.263 Angle : 0.582 11.667 16916 Z= 0.283 Chirality : 0.041 0.154 1808 Planarity : 0.004 0.041 2080 Dihedral : 6.675 73.434 1620 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 1.81 % Allowed : 10.13 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.21), residues: 1474 helix: -0.22 (0.17), residues: 974 sheet: None (None), residues: 0 loop : -2.28 (0.24), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 342 HIS 0.006 0.001 HIS B 541 PHE 0.029 0.001 PHE B 471 TYR 0.017 0.001 TYR A 328 ARG 0.004 0.000 ARG A 516 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 87 time to evaluate : 1.423 Fit side-chains REVERT: A 471 PHE cc_start: 0.7986 (OUTLIER) cc_final: 0.7774 (p90) REVERT: A 715 GLU cc_start: 0.7638 (tp30) cc_final: 0.7338 (tp30) REVERT: B 471 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.7742 (p90) outliers start: 22 outliers final: 16 residues processed: 101 average time/residue: 0.2341 time to fit residues: 36.6035 Evaluate side-chains 104 residues out of total 1214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 86 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 605 MET Chi-restraints excluded: chain B residue 4 TYR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 471 PHE Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 605 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 2.9990 chunk 128 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 143 optimal weight: 5.9990 chunk 118 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 277 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12368 Z= 0.238 Angle : 0.559 11.204 16916 Z= 0.274 Chirality : 0.041 0.151 1808 Planarity : 0.004 0.041 2080 Dihedral : 6.662 73.044 1620 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.81 % Allowed : 10.87 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.22), residues: 1474 helix: -0.11 (0.17), residues: 972 sheet: None (None), residues: 0 loop : -2.22 (0.24), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 342 HIS 0.006 0.001 HIS B 541 PHE 0.026 0.001 PHE A 471 TYR 0.014 0.001 TYR B 328 ARG 0.003 0.000 ARG A 516 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 95 time to evaluate : 1.377 Fit side-chains REVERT: A 365 LYS cc_start: 0.4732 (mttt) cc_final: 0.4281 (mmmm) REVERT: A 471 PHE cc_start: 0.7991 (OUTLIER) cc_final: 0.7763 (p90) REVERT: B 471 PHE cc_start: 0.8014 (OUTLIER) cc_final: 0.7780 (p90) outliers start: 22 outliers final: 18 residues processed: 108 average time/residue: 0.2257 time to fit residues: 36.9521 Evaluate side-chains 113 residues out of total 1214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 93 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 605 MET Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain B residue 4 TYR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 471 PHE Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 605 MET Chi-restraints excluded: chain B residue 685 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 104 optimal weight: 0.8980 chunk 120 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 142 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 277 GLN A 581 GLN B 178 ASN B 277 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12368 Z= 0.158 Angle : 0.507 8.970 16916 Z= 0.252 Chirality : 0.038 0.140 1808 Planarity : 0.004 0.040 2080 Dihedral : 6.522 72.544 1620 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.65 % Allowed : 11.70 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.22), residues: 1474 helix: 0.11 (0.17), residues: 976 sheet: None (None), residues: 0 loop : -2.09 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 342 HIS 0.005 0.001 HIS B 541 PHE 0.019 0.001 PHE A 471 TYR 0.012 0.001 TYR A 472 ARG 0.002 0.000 ARG A 516 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 101 time to evaluate : 1.427 Fit side-chains REVERT: A 471 PHE cc_start: 0.7813 (OUTLIER) cc_final: 0.7588 (p90) REVERT: B 471 PHE cc_start: 0.7820 (OUTLIER) cc_final: 0.7612 (p90) outliers start: 20 outliers final: 15 residues processed: 114 average time/residue: 0.2206 time to fit residues: 38.4089 Evaluate side-chains 115 residues out of total 1214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 98 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 605 MET Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain B residue 4 TYR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 471 PHE Chi-restraints excluded: chain B residue 605 MET Chi-restraints excluded: chain B residue 685 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 0.0010 chunk 85 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 70 optimal weight: 0.0670 chunk 13 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 chunk 129 optimal weight: 0.4980 overall best weight: 0.8526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN B 277 GLN B 581 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12368 Z= 0.155 Angle : 0.499 8.369 16916 Z= 0.248 Chirality : 0.038 0.138 1808 Planarity : 0.004 0.040 2080 Dihedral : 6.433 72.872 1620 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.06 % Allowed : 11.37 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.22), residues: 1474 helix: 0.27 (0.17), residues: 988 sheet: None (None), residues: 0 loop : -2.04 (0.25), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 342 HIS 0.006 0.001 HIS B 541 PHE 0.019 0.001 PHE A 471 TYR 0.011 0.001 TYR B 472 ARG 0.003 0.000 ARG A 516 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 111 time to evaluate : 1.449 Fit side-chains REVERT: A 379 PHE cc_start: 0.8172 (OUTLIER) cc_final: 0.7052 (m-80) REVERT: A 471 PHE cc_start: 0.7780 (OUTLIER) cc_final: 0.7562 (p90) REVERT: A 496 PHE cc_start: 0.8553 (OUTLIER) cc_final: 0.7253 (t80) REVERT: B 379 PHE cc_start: 0.8199 (OUTLIER) cc_final: 0.7076 (m-80) REVERT: B 471 PHE cc_start: 0.7765 (OUTLIER) cc_final: 0.7541 (p90) REVERT: B 496 PHE cc_start: 0.8602 (OUTLIER) cc_final: 0.7277 (t80) outliers start: 25 outliers final: 15 residues processed: 124 average time/residue: 0.2118 time to fit residues: 40.1780 Evaluate side-chains 127 residues out of total 1214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 106 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 379 PHE Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 496 PHE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 605 MET Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 366 PHE Chi-restraints excluded: chain B residue 379 PHE Chi-restraints excluded: chain B residue 471 PHE Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 605 MET Chi-restraints excluded: chain B residue 685 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 chunk 57 optimal weight: 0.5980 chunk 104 optimal weight: 0.0020 chunk 40 optimal weight: 5.9990 chunk 120 optimal weight: 0.1980 chunk 125 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 140 optimal weight: 0.9980 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN B 277 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12368 Z= 0.160 Angle : 0.504 8.610 16916 Z= 0.249 Chirality : 0.038 0.138 1808 Planarity : 0.004 0.040 2080 Dihedral : 6.434 72.888 1620 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.81 % Allowed : 11.86 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.22), residues: 1474 helix: 0.40 (0.17), residues: 986 sheet: None (None), residues: 0 loop : -1.99 (0.25), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 342 HIS 0.006 0.001 HIS B 541 PHE 0.019 0.001 PHE B 471 TYR 0.012 0.001 TYR A 472 ARG 0.003 0.000 ARG A 516 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 112 time to evaluate : 1.363 Fit side-chains REVERT: A 379 PHE cc_start: 0.8178 (OUTLIER) cc_final: 0.6994 (m-80) REVERT: A 471 PHE cc_start: 0.7713 (OUTLIER) cc_final: 0.7491 (p90) REVERT: A 496 PHE cc_start: 0.8535 (OUTLIER) cc_final: 0.7303 (t80) REVERT: B 379 PHE cc_start: 0.8202 (OUTLIER) cc_final: 0.7078 (m-80) REVERT: B 471 PHE cc_start: 0.7702 (OUTLIER) cc_final: 0.7472 (p90) REVERT: B 496 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.7273 (t80) outliers start: 22 outliers final: 14 residues processed: 124 average time/residue: 0.2146 time to fit residues: 40.8486 Evaluate side-chains 129 residues out of total 1214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 109 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 379 PHE Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 496 PHE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 605 MET Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 379 PHE Chi-restraints excluded: chain B residue 471 PHE Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 605 MET Chi-restraints excluded: chain B residue 685 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 135 optimal weight: 0.0980 chunk 117 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 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 277 GLN B 277 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12368 Z= 0.175 Angle : 0.512 9.046 16916 Z= 0.253 Chirality : 0.039 0.140 1808 Planarity : 0.004 0.040 2080 Dihedral : 6.431 73.015 1620 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.81 % Allowed : 11.86 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.22), residues: 1474 helix: 0.45 (0.17), residues: 986 sheet: None (None), residues: 0 loop : -1.96 (0.25), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 342 HIS 0.006 0.001 HIS B 541 PHE 0.021 0.001 PHE B 471 TYR 0.012 0.001 TYR A 472 ARG 0.003 0.000 ARG A 516 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 110 time to evaluate : 1.293 Fit side-chains REVERT: A 379 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.7017 (m-80) REVERT: A 471 PHE cc_start: 0.7736 (OUTLIER) cc_final: 0.7506 (p90) REVERT: A 496 PHE cc_start: 0.8543 (OUTLIER) cc_final: 0.7299 (t80) REVERT: B 379 PHE cc_start: 0.8186 (OUTLIER) cc_final: 0.7007 (m-80) REVERT: B 471 PHE cc_start: 0.7719 (OUTLIER) cc_final: 0.7480 (p90) REVERT: B 496 PHE cc_start: 0.8552 (OUTLIER) cc_final: 0.7232 (t80) outliers start: 22 outliers final: 15 residues processed: 121 average time/residue: 0.2167 time to fit residues: 39.8692 Evaluate side-chains 130 residues out of total 1214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 109 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 379 PHE Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 496 PHE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 605 MET Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 366 PHE Chi-restraints excluded: chain B residue 379 PHE Chi-restraints excluded: chain B residue 471 PHE Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 605 MET Chi-restraints excluded: chain B residue 685 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 8.9990 chunk 108 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 117 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 120 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN B 277 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.105659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.084095 restraints weight = 15777.656| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 1.59 r_work: 0.2716 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2597 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12368 Z= 0.203 Angle : 0.535 10.264 16916 Z= 0.262 Chirality : 0.040 0.145 1808 Planarity : 0.004 0.040 2080 Dihedral : 6.507 73.127 1620 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.89 % Allowed : 11.94 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.22), residues: 1474 helix: 0.42 (0.17), residues: 986 sheet: None (None), residues: 0 loop : -1.97 (0.25), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 342 HIS 0.006 0.001 HIS B 541 PHE 0.024 0.001 PHE B 471 TYR 0.014 0.001 TYR A 328 ARG 0.003 0.000 ARG A 516 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2296.38 seconds wall clock time: 42 minutes 34.77 seconds (2554.77 seconds total)