Starting phenix.real_space_refine on Fri Feb 23 01:47:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rr7_4986/02_2024/6rr7_4986_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rr7_4986/02_2024/6rr7_4986.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rr7_4986/02_2024/6rr7_4986_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rr7_4986/02_2024/6rr7_4986_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rr7_4986/02_2024/6rr7_4986_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rr7_4986/02_2024/6rr7_4986.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rr7_4986/02_2024/6rr7_4986.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rr7_4986/02_2024/6rr7_4986_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rr7_4986/02_2024/6rr7_4986_trim_updated.pdb" } resolution = 3.01 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= 0.009 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 P 32 5.49 5 S 128 5.16 5 C 11395 2.51 5 N 3202 2.21 5 O 3532 1.98 5 H 18001 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 23": "OE1" <-> "OE2" Residue "A ASP 66": "OD1" <-> "OD2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A GLU 114": "OE1" <-> "OE2" Residue "A ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 124": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A ASP 189": "OD1" <-> "OD2" Residue "A ARG 204": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 269": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 272": "OD1" <-> "OD2" Residue "A ARG 279": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 356": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 377": "OE1" <-> "OE2" Residue "A ARG 454": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 531": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 682": "OD1" <-> "OD2" Residue "A GLU 688": "OE1" <-> "OE2" Residue "A PHE 707": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 187": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 233": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 238": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 267": "OE1" <-> "OE2" Residue "B GLU 331": "OE1" <-> "OE2" Residue "B ASP 439": "OD1" <-> "OD2" Residue "B ARG 563": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 572": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 614": "OE1" <-> "OE2" Residue "B ARG 680": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 685": "OD1" <-> "OD2" Residue "B ARG 707": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 716": "OE1" <-> "OE2" Residue "B ARG 734": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 751": "OE1" <-> "OE2" Residue "B ARG 755": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 46": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 101": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 209": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 275": "OD1" <-> "OD2" Residue "C ARG 340": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 362": "OE1" <-> "OE2" Residue "C ARG 375": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 379": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 380": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 390": "OD1" <-> "OD2" Residue "C ARG 423": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 436": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 441": "OD1" <-> "OD2" Residue "C TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 500": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 503": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 525": "OE1" <-> "OE2" Residue "C GLU 558": "OE1" <-> "OE2" Residue "C GLU 578": "OE1" <-> "OE2" Residue "C ARG 650": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 720": "OE1" <-> "OE2" Residue "C ARG 737": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 36290 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 11578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 11578 Classifications: {'peptide': 716} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 31, 'TRANS': 684} Chain: "B" Number of atoms: 11887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 744, 11887 Classifications: {'peptide': 744} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 32, 'TRANS': 711} Chain breaks: 1 Chain: "C" Number of atoms: 11832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 11832 Classifications: {'peptide': 737} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 28, 'TRANS': 708} Chain: "F" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 187 Unusual residues: {'M7G': 1} Classifications: {'RNA': 5, 'undetermined': 1} Modifications used: {'3*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 3} Link IDs: {'rna2p': 4, None: 1} Not linked: pdbres="M7G F 0 " pdbres=" A F 1 " Chain: "E" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 346 Classifications: {'RNA': 11} Modifications used: {'3*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 3, 'rna3p': 7} Chain: "D" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 460 Classifications: {'RNA': 14} Modifications used: {'3*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 10} Time building chain proxies: 15.36, per 1000 atoms: 0.42 Number of scatterers: 36290 At special positions: 0 Unit cell: (106.33, 141.05, 141.05, 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) S 128 16.00 P 32 15.00 O 3532 8.00 N 3202 7.00 C 11395 6.00 H 18001 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 26.94 Conformation dependent library (CDL) restraints added in 3.4 seconds 4378 Ramachandran restraints generated. 2189 Oldfield, 0 Emsley, 2189 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4138 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 85 helices and 22 sheets defined 39.2% alpha, 10.1% beta 6 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 17.99 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 Processing helix chain 'A' and resid 11 through 24 Processing helix chain 'A' and resid 33 through 49 Processing helix chain 'A' and resid 84 through 97 Processing helix chain 'A' and resid 127 through 137 removed outlier: 4.414A pdb=" N LEU A 132 " --> pdb=" O HIS A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 185 removed outlier: 4.217A pdb=" N ASN A 184 " --> pdb=" O GLN A 180 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 191 Processing helix chain 'A' and resid 209 through 216 removed outlier: 4.432A pdb=" N LEU A 214 " --> pdb=" O MET A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 234 Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 303 through 312 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.855A pdb=" N GLU A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN A 350 " --> pdb=" O GLN A 346 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLU A 351 " --> pdb=" O ASP A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 381 through 383 No H-bonds generated for 'chain 'A' and resid 381 through 383' Processing helix chain 'A' and resid 406 through 414 Processing helix chain 'A' and resid 434 through 451 Processing helix chain 'A' and resid 454 through 475 Processing helix chain 'A' and resid 534 through 536 No H-bonds generated for 'chain 'A' and resid 534 through 536' Processing helix chain 'A' and resid 572 through 578 Processing helix chain 'A' and resid 581 through 600 removed outlier: 4.148A pdb=" N SER A 588 " --> pdb=" O LEU A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 614 Processing helix chain 'A' and resid 633 through 649 Processing helix chain 'A' and resid 653 through 673 removed outlier: 3.860A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 690 Processing helix chain 'A' and resid 698 through 713 Processing helix chain 'B' and resid 6 through 10 Processing helix chain 'B' and resid 18 through 21 Processing helix chain 'B' and resid 36 through 48 Processing helix chain 'B' and resid 85 through 98 Processing helix chain 'B' and resid 102 through 116 Processing helix chain 'B' and resid 119 through 122 Processing helix chain 'B' and resid 139 through 153 Processing helix chain 'B' and resid 157 through 160 Processing helix chain 'B' and resid 163 through 172 Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 249 through 265 removed outlier: 3.918A pdb=" N LYS B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 292 Processing helix chain 'B' and resid 309 through 312 No H-bonds generated for 'chain 'B' and resid 309 through 312' Processing helix chain 'B' and resid 315 through 325 Processing helix chain 'B' and resid 331 through 336 Processing helix chain 'B' and resid 339 through 343 Processing helix chain 'B' and resid 370 through 372 No H-bonds generated for 'chain 'B' and resid 370 through 372' Processing helix chain 'B' and resid 383 through 395 Proline residue: B 394 - end of helix Processing helix chain 'B' and resid 413 through 426 removed outlier: 3.750A pdb=" N LEU B 426 " --> pdb=" O SER B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 471 Processing helix chain 'B' and resid 509 through 511 No H-bonds generated for 'chain 'B' and resid 509 through 511' Processing helix chain 'B' and resid 519 through 535 removed outlier: 3.651A pdb=" N ILE B 530 " --> pdb=" O GLY B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 559 Processing helix chain 'B' and resid 575 through 582 Processing helix chain 'B' and resid 601 through 603 No H-bonds generated for 'chain 'B' and resid 601 through 603' Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 637 through 639 No H-bonds generated for 'chain 'B' and resid 637 through 639' Processing helix chain 'B' and resid 674 through 676 No H-bonds generated for 'chain 'B' and resid 674 through 676' Processing helix chain 'B' and resid 678 through 680 No H-bonds generated for 'chain 'B' and resid 678 through 680' Processing helix chain 'B' and resid 682 through 699 Processing helix chain 'B' and resid 701 through 704 removed outlier: 3.883A pdb=" N SER B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 701 through 704' Processing helix chain 'B' and resid 714 through 731 Processing helix chain 'B' and resid 737 through 754 Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 15 through 21 Processing helix chain 'C' and resid 28 through 33 removed outlier: 4.253A pdb=" N LYS C 33 " --> pdb=" O ALA C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 50 Processing helix chain 'C' and resid 61 through 65 Processing helix chain 'C' and resid 94 through 102 Processing helix chain 'C' and resid 111 through 114 No H-bonds generated for 'chain 'C' and resid 111 through 114' Processing helix chain 'C' and resid 116 through 126 Processing helix chain 'C' and resid 158 through 167 Processing helix chain 'C' and resid 180 through 192 Processing helix chain 'C' and resid 200 through 211 Processing helix chain 'C' and resid 232 through 235 No H-bonds generated for 'chain 'C' and resid 232 through 235' Processing helix chain 'C' and resid 252 through 272 removed outlier: 4.037A pdb=" N VAL C 272 " --> pdb=" O ARG C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 285 Processing helix chain 'C' and resid 294 through 300 Processing helix chain 'C' and resid 306 through 314 Processing helix chain 'C' and resid 391 through 405 Processing helix chain 'C' and resid 408 through 413 removed outlier: 4.023A pdb=" N ALA C 413 " --> pdb=" O CYS C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 439 removed outlier: 3.742A pdb=" N GLN C 439 " --> pdb=" O LEU C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 447 Processing helix chain 'C' and resid 457 through 459 No H-bonds generated for 'chain 'C' and resid 457 through 459' Processing helix chain 'C' and resid 542 through 555 Processing helix chain 'C' and resid 557 through 563 removed outlier: 4.354A pdb=" N ILE C 562 " --> pdb=" O GLU C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 572 No H-bonds generated for 'chain 'C' and resid 569 through 572' Processing helix chain 'C' and resid 578 through 581 No H-bonds generated for 'chain 'C' and resid 578 through 581' Processing helix chain 'C' and resid 589 through 605 Processing helix chain 'C' and resid 612 through 618 Processing sheet with id= A, first strand: chain 'A' and resid 76 through 78 removed outlier: 7.402A pdb=" N HIS A 144 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N GLY A 121 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N HIS A 146 " --> pdb=" O GLY A 121 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N THR A 123 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N PHE A 148 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 321 through 324 removed outlier: 3.534A pdb=" N TYR A 321 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL A 542 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N MET A 561 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ASP A 547 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ARG A 559 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 619 through 624 removed outlier: 7.085A pdb=" N GLU A 629 " --> pdb=" O ILE A 621 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N GLU A 623 " --> pdb=" O GLY A 627 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLY A 627 " --> pdb=" O GLU A 623 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 54 through 57 Processing sheet with id= E, first strand: chain 'B' and resid 128 through 130 removed outlier: 3.623A pdb=" N ARG B 135 " --> pdb=" O ASP B 130 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 179 through 184 Processing sheet with id= G, first strand: chain 'B' and resid 225 through 228 Processing sheet with id= H, first strand: chain 'B' and resid 483 through 486 Processing sheet with id= I, first strand: chain 'B' and resid 348 through 350 Processing sheet with id= J, first strand: chain 'B' and resid 355 through 359 Processing sheet with id= K, first strand: chain 'B' and resid 489 through 492 Processing sheet with id= L, first strand: chain 'B' and resid 643 through 645 Processing sheet with id= M, first strand: chain 'C' and resid 57 through 59 Processing sheet with id= N, first strand: chain 'C' and resid 133 through 135 Processing sheet with id= O, first strand: chain 'C' and resid 287 through 289 Processing sheet with id= P, first strand: chain 'C' and resid 323 through 325 Processing sheet with id= Q, first strand: chain 'C' and resid 342 through 344 Processing sheet with id= R, first strand: chain 'C' and resid 331 through 334 removed outlier: 3.599A pdb=" N LYS C 331 " --> pdb=" O THR C 364 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLU C 362 " --> pdb=" O THR C 333 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ALA C 377 " --> pdb=" O LEU C 381 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N LEU C 381 " --> pdb=" O ALA C 377 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 635 through 640 Processing sheet with id= T, first strand: chain 'C' and resid 656 through 658 Processing sheet with id= U, first strand: chain 'C' and resid 722 through 726 removed outlier: 3.651A pdb=" N LEU C 733 " --> pdb=" O GLY C 698 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY C 698 " --> pdb=" O LEU C 733 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N MET C 735 " --> pdb=" O ILE C 696 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ILE C 696 " --> pdb=" O MET C 735 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 141 through 148 removed outlier: 6.848A pdb=" N LYS C 214 " --> pdb=" O ILE C 147 " (cutoff:3.500A) 656 hydrogen bonds defined for protein. 1797 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 32 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 13.42 Time building geometry restraints manager: 28.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 17970 1.03 - 1.22: 50 1.22 - 1.42: 7760 1.42 - 1.61: 10696 1.61 - 1.81: 228 Bond restraints: 36704 Sorted by residual: bond pdb=" C3' M7G F 0 " pdb=" C4' M7G F 0 " ideal model delta sigma weight residual 1.615 1.306 0.309 2.00e-02 2.50e+03 2.39e+02 bond pdb=" C2' M7G F 0 " pdb=" C3' M7G F 0 " ideal model delta sigma weight residual 1.236 1.540 -0.304 2.00e-02 2.50e+03 2.30e+02 bond pdb=" C2' M7G F 0 " pdb=" O2' M7G F 0 " ideal model delta sigma weight residual 1.505 1.355 0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" C1' M7G F 0 " pdb=" C2' M7G F 0 " ideal model delta sigma weight residual 1.656 1.531 0.125 2.00e-02 2.50e+03 3.88e+01 bond pdb=" C4' M7G F 0 " pdb=" O4' M7G F 0 " ideal model delta sigma weight residual 1.495 1.608 -0.113 2.00e-02 2.50e+03 3.20e+01 ... (remaining 36699 not shown) Histogram of bond angle deviations from ideal: 96.76 - 104.26: 423 104.26 - 111.76: 40789 111.76 - 119.26: 10027 119.26 - 126.76: 14755 126.76 - 134.26: 314 Bond angle restraints: 66308 Sorted by residual: angle pdb=" N VAL A 127 " pdb=" CA VAL A 127 " pdb=" C VAL A 127 " ideal model delta sigma weight residual 110.74 114.74 -4.00 9.10e-01 1.21e+00 1.93e+01 angle pdb=" CA LYS B 480 " pdb=" CB LYS B 480 " pdb=" CG LYS B 480 " ideal model delta sigma weight residual 114.10 120.78 -6.68 2.00e+00 2.50e-01 1.11e+01 angle pdb=" C2' A D 4 " pdb=" C1' A D 4 " pdb=" N9 A D 4 " ideal model delta sigma weight residual 112.00 116.84 -4.84 1.50e+00 4.44e-01 1.04e+01 angle pdb=" N GLN A 481 " pdb=" CA GLN A 481 " pdb=" C GLN A 481 " ideal model delta sigma weight residual 108.75 113.66 -4.91 1.71e+00 3.42e-01 8.24e+00 angle pdb=" C2' U E 11 " pdb=" C1' U E 11 " pdb=" N1 U E 11 " ideal model delta sigma weight residual 112.00 116.14 -4.14 1.50e+00 4.44e-01 7.63e+00 ... (remaining 66303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.80: 16615 34.80 - 69.59: 579 69.59 - 104.39: 31 104.39 - 139.19: 0 139.19 - 173.99: 2 Dihedral angle restraints: 17227 sinusoidal: 9793 harmonic: 7434 Sorted by residual: dihedral pdb=" O4' C F 4 " pdb=" C1' C F 4 " pdb=" N1 C F 4 " pdb=" C2 C F 4 " ideal model delta sinusoidal sigma weight residual -128.00 45.99 -173.99 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' U F 3 " pdb=" C1' U F 3 " pdb=" N1 U F 3 " pdb=" C2 U F 3 " ideal model delta sinusoidal sigma weight residual -128.00 37.85 -165.85 1 1.70e+01 3.46e-03 6.54e+01 dihedral pdb=" CA GLU A 126 " pdb=" C GLU A 126 " pdb=" N VAL A 127 " pdb=" CA VAL A 127 " ideal model delta harmonic sigma weight residual -180.00 -150.66 -29.34 0 5.00e+00 4.00e-02 3.44e+01 ... (remaining 17224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1747 0.043 - 0.087: 803 0.087 - 0.130: 223 0.130 - 0.174: 33 0.174 - 0.217: 9 Chirality restraints: 2815 Sorted by residual: chirality pdb=" C1' U E 11 " pdb=" O4' U E 11 " pdb=" C2' U E 11 " pdb=" N1 U E 11 " both_signs ideal model delta sigma weight residual False 2.47 2.25 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CB VAL B 170 " pdb=" CA VAL B 170 " pdb=" CG1 VAL B 170 " pdb=" CG2 VAL B 170 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB ILE A 407 " pdb=" CA ILE A 407 " pdb=" CG1 ILE A 407 " pdb=" CG2 ILE A 407 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 2812 not shown) Planarity restraints: 5287 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 464 " 0.051 5.00e-02 4.00e+02 7.83e-02 9.80e+00 pdb=" N PRO C 465 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO C 465 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 465 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A D 4 " -0.038 2.00e-02 2.50e+03 1.59e-02 8.25e+00 pdb=" N9 A D 4 " 0.041 2.00e-02 2.50e+03 pdb=" C8 A D 4 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A D 4 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A D 4 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A D 4 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A D 4 " -0.011 2.00e-02 2.50e+03 pdb=" N1 A D 4 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A D 4 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A D 4 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A D 4 " 0.001 2.00e-02 2.50e+03 pdb=" H8 A D 4 " 0.003 2.00e-02 2.50e+03 pdb=" H2 A D 4 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 393 " 0.041 5.00e-02 4.00e+02 6.24e-02 6.23e+00 pdb=" N PRO B 394 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 394 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 394 " 0.035 5.00e-02 4.00e+02 ... (remaining 5284 not shown) Histogram of nonbonded interaction distances: 1.25 - 1.92: 135 1.92 - 2.59: 40431 2.59 - 3.26: 104930 3.26 - 3.93: 136156 3.93 - 4.60: 223566 Nonbonded interactions: 505218 Sorted by model distance: nonbonded pdb=" O3B M7G F 0 " pdb=" OP2 A F 1 " model vdw 1.252 2.800 nonbonded pdb=" O3B M7G F 0 " pdb=" P A F 1 " model vdw 1.583 3.200 nonbonded pdb=" O LEU A 655 " pdb=" HG SER A 659 " model vdw 1.646 1.850 nonbonded pdb=" OD1 ASN B 276 " pdb="HH11 ARG C 142 " model vdw 1.663 1.850 nonbonded pdb=" O PHE A 658 " pdb=" HG SER A 662 " model vdw 1.672 1.850 ... (remaining 505213 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.520 Extract box with map and model: 5.350 Check model and map are aligned: 0.550 Set scattering table: 0.330 Process input model: 118.970 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.090 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 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 : 0.010 0.309 18703 Z= 0.629 Angle : 0.847 7.471 25368 Z= 0.443 Chirality : 0.052 0.217 2815 Planarity : 0.006 0.078 3163 Dihedral : 15.710 173.986 7343 Min Nonbonded Distance : 1.252 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % 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 (0.15), residues: 2189 helix: -1.82 (0.14), residues: 927 sheet: -2.36 (0.27), residues: 274 loop : -2.95 (0.16), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 368 HIS 0.007 0.001 HIS A 326 PHE 0.022 0.002 PHE A 520 TYR 0.020 0.002 TYR A 540 ARG 0.009 0.001 ARG A 663 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4378 Ramachandran restraints generated. 2189 Oldfield, 0 Emsley, 2189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4378 Ramachandran restraints generated. 2189 Oldfield, 0 Emsley, 2189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 371 time to evaluate : 3.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 ILE cc_start: 0.8184 (pt) cc_final: 0.7973 (mm) REVERT: C 1 MET cc_start: 0.6481 (tpp) cc_final: 0.6257 (tpt) REVERT: C 177 LEU cc_start: 0.7973 (mt) cc_final: 0.7679 (mp) outliers start: 0 outliers final: 0 residues processed: 371 average time/residue: 1.0076 time to fit residues: 510.4466 Evaluate side-chains 270 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 2.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 3.9990 chunk 166 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 104 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 ASN A 217 GLN A 228 ASN B 116 GLN B 137 GLN B 153 ASN B 452 ASN ** B 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18703 Z= 0.158 Angle : 0.527 4.738 25368 Z= 0.279 Chirality : 0.039 0.173 2815 Planarity : 0.004 0.059 3163 Dihedral : 11.494 174.840 2864 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.67 % Allowed : 7.18 % Favored : 92.15 % 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: -2.25 (0.16), residues: 2189 helix: -0.42 (0.16), residues: 932 sheet: -1.81 (0.29), residues: 274 loop : -2.46 (0.17), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 368 HIS 0.003 0.001 HIS B 184 PHE 0.013 0.001 PHE B 185 TYR 0.011 0.001 TYR C 360 ARG 0.006 0.000 ARG C 503 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4378 Ramachandran restraints generated. 2189 Oldfield, 0 Emsley, 2189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4378 Ramachandran restraints generated. 2189 Oldfield, 0 Emsley, 2189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 279 time to evaluate : 2.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 179 MET cc_start: 0.7325 (tpt) cc_final: 0.6999 (tpt) REVERT: B 232 GLU cc_start: 0.6562 (mt-10) cc_final: 0.6263 (mt-10) REVERT: C 1 MET cc_start: 0.6539 (tpp) cc_final: 0.6299 (tpt) REVERT: C 51 MET cc_start: 0.7964 (mmm) cc_final: 0.7747 (mmp) REVERT: C 300 GLN cc_start: 0.6907 (OUTLIER) cc_final: 0.6476 (mp10) outliers start: 13 outliers final: 9 residues processed: 285 average time/residue: 0.8907 time to fit residues: 355.8918 Evaluate side-chains 274 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 264 time to evaluate : 2.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 300 GLN Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 409 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 111 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 166 optimal weight: 0.9990 chunk 136 optimal weight: 0.0980 chunk 55 optimal weight: 9.9990 chunk 200 optimal weight: 3.9990 chunk 216 optimal weight: 7.9990 chunk 178 optimal weight: 4.9990 chunk 198 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 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 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 GLN A 228 ASN B 306 ASN ** B 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 9 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18703 Z= 0.242 Angle : 0.530 4.746 25368 Z= 0.281 Chirality : 0.040 0.166 2815 Planarity : 0.004 0.055 3163 Dihedral : 11.419 175.037 2864 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.87 % Allowed : 8.46 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.17), residues: 2189 helix: 0.05 (0.17), residues: 937 sheet: -1.49 (0.30), residues: 274 loop : -2.19 (0.18), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 438 HIS 0.002 0.001 HIS A 535 PHE 0.014 0.001 PHE B 185 TYR 0.011 0.001 TYR C 360 ARG 0.004 0.000 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4378 Ramachandran restraints generated. 2189 Oldfield, 0 Emsley, 2189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4378 Ramachandran restraints generated. 2189 Oldfield, 0 Emsley, 2189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 266 time to evaluate : 2.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8578 (mp) REVERT: B 179 MET cc_start: 0.7523 (tpt) cc_final: 0.7087 (tpt) REVERT: B 232 GLU cc_start: 0.6484 (mt-10) cc_final: 0.6141 (mt-10) outliers start: 17 outliers final: 12 residues processed: 272 average time/residue: 0.9240 time to fit residues: 350.8743 Evaluate side-chains 269 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 256 time to evaluate : 2.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 300 GLN Chi-restraints excluded: chain C residue 409 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 3.9990 chunk 150 optimal weight: 0.0980 chunk 103 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 chunk 200 optimal weight: 3.9990 chunk 212 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 190 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 ASN ** B 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18703 Z= 0.171 Angle : 0.484 5.283 25368 Z= 0.257 Chirality : 0.038 0.168 2815 Planarity : 0.004 0.047 3163 Dihedral : 11.255 175.292 2864 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.67 % Allowed : 9.38 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.17), residues: 2189 helix: 0.44 (0.17), residues: 943 sheet: -1.22 (0.30), residues: 276 loop : -1.94 (0.18), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 368 HIS 0.002 0.001 HIS A 326 PHE 0.012 0.001 PHE B 185 TYR 0.010 0.001 TYR C 360 ARG 0.004 0.000 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4378 Ramachandran restraints generated. 2189 Oldfield, 0 Emsley, 2189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4378 Ramachandran restraints generated. 2189 Oldfield, 0 Emsley, 2189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 257 time to evaluate : 2.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 GLN cc_start: 0.8432 (mt0) cc_final: 0.8212 (mt0) REVERT: A 512 ARG cc_start: 0.6590 (OUTLIER) cc_final: 0.5973 (mtm180) REVERT: B 92 MET cc_start: 0.8137 (mmm) cc_final: 0.7142 (mmp) REVERT: B 179 MET cc_start: 0.7573 (tpt) cc_final: 0.7084 (tpt) REVERT: B 523 MET cc_start: 0.7741 (tpt) cc_final: 0.7520 (tpt) REVERT: B 691 LYS cc_start: 0.8060 (mttt) cc_final: 0.7849 (mttm) REVERT: B 744 MET cc_start: 0.7806 (mmm) cc_final: 0.7413 (mmm) outliers start: 13 outliers final: 10 residues processed: 261 average time/residue: 0.8940 time to fit residues: 326.0155 Evaluate side-chains 264 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 253 time to evaluate : 2.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 512 ARG Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 300 GLN Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain C residue 540 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 177 optimal weight: 4.9990 chunk 120 optimal weight: 0.0770 chunk 3 optimal weight: 10.0000 chunk 158 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 chunk 146 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 190 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 ASN B 642 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18703 Z= 0.281 Angle : 0.537 7.753 25368 Z= 0.285 Chirality : 0.041 0.162 2815 Planarity : 0.004 0.053 3163 Dihedral : 11.312 174.551 2864 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.03 % Allowed : 9.90 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.17), residues: 2189 helix: 0.40 (0.17), residues: 942 sheet: -1.11 (0.30), residues: 276 loop : -1.91 (0.18), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 438 HIS 0.003 0.001 HIS B 605 PHE 0.013 0.001 PHE A 520 TYR 0.011 0.001 TYR B 559 ARG 0.005 0.000 ARG A 663 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4378 Ramachandran restraints generated. 2189 Oldfield, 0 Emsley, 2189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4378 Ramachandran restraints generated. 2189 Oldfield, 0 Emsley, 2189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 253 time to evaluate : 2.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8662 (mt) REVERT: A 248 GLN cc_start: 0.8434 (mt0) cc_final: 0.8194 (mt0) REVERT: B 92 MET cc_start: 0.8227 (mmm) cc_final: 0.7297 (mmp) REVERT: B 179 MET cc_start: 0.7697 (tpt) cc_final: 0.7165 (tpt) REVERT: B 523 MET cc_start: 0.7857 (tpt) cc_final: 0.7651 (tpt) REVERT: B 707 ARG cc_start: 0.8246 (ttp-110) cc_final: 0.8036 (ttp-110) REVERT: B 744 MET cc_start: 0.8074 (mmm) cc_final: 0.7843 (mmm) REVERT: C 51 MET cc_start: 0.8877 (mmp) cc_final: 0.8432 (mmp) REVERT: C 65 GLU cc_start: 0.7489 (pt0) cc_final: 0.7257 (pt0) outliers start: 20 outliers final: 17 residues processed: 260 average time/residue: 0.8701 time to fit residues: 318.3906 Evaluate side-chains 266 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 248 time to evaluate : 2.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 300 GLN Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain C residue 540 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 71 optimal weight: 1.9990 chunk 191 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 212 optimal weight: 5.9990 chunk 176 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18703 Z= 0.240 Angle : 0.510 7.323 25368 Z= 0.272 Chirality : 0.040 0.171 2815 Planarity : 0.004 0.053 3163 Dihedral : 11.242 174.384 2864 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.08 % Allowed : 10.72 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.17), residues: 2189 helix: 0.49 (0.17), residues: 950 sheet: -1.07 (0.30), residues: 276 loop : -1.81 (0.18), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 368 HIS 0.003 0.001 HIS A 510 PHE 0.013 0.001 PHE A 520 TYR 0.010 0.001 TYR C 360 ARG 0.006 0.000 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4378 Ramachandran restraints generated. 2189 Oldfield, 0 Emsley, 2189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4378 Ramachandran restraints generated. 2189 Oldfield, 0 Emsley, 2189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 250 time to evaluate : 2.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8661 (mt) REVERT: A 248 GLN cc_start: 0.8482 (mt0) cc_final: 0.8233 (mt0) REVERT: A 285 MET cc_start: 0.8335 (ptm) cc_final: 0.8096 (ptm) REVERT: A 523 MET cc_start: 0.8625 (mtt) cc_final: 0.8382 (mtt) REVERT: B 92 MET cc_start: 0.8219 (mmm) cc_final: 0.7352 (mmp) REVERT: B 179 MET cc_start: 0.7774 (tpt) cc_final: 0.7228 (tpt) REVERT: B 523 MET cc_start: 0.7870 (tpt) cc_final: 0.7658 (tpt) REVERT: B 707 ARG cc_start: 0.8267 (ttp-110) cc_final: 0.8062 (ttp-110) REVERT: B 744 MET cc_start: 0.8180 (mmm) cc_final: 0.7925 (mmm) REVERT: C 51 MET cc_start: 0.8887 (mmp) cc_final: 0.8524 (mmp) REVERT: C 628 GLN cc_start: 0.6833 (mm110) cc_final: 0.6575 (mm-40) REVERT: C 648 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8480 (mt) outliers start: 21 outliers final: 19 residues processed: 259 average time/residue: 0.8889 time to fit residues: 322.4878 Evaluate side-chains 265 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 244 time to evaluate : 2.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 300 GLN Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 648 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 0.0570 chunk 23 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 120 optimal weight: 0.0670 chunk 179 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 212 optimal weight: 5.9990 chunk 132 optimal weight: 0.5980 chunk 129 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 18703 Z= 0.157 Angle : 0.471 4.777 25368 Z= 0.250 Chirality : 0.038 0.158 2815 Planarity : 0.004 0.047 3163 Dihedral : 11.127 174.704 2864 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.77 % Allowed : 11.18 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.18), residues: 2189 helix: 0.72 (0.17), residues: 949 sheet: -0.93 (0.30), residues: 276 loop : -1.70 (0.18), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 368 HIS 0.003 0.001 HIS A 326 PHE 0.010 0.001 PHE B 185 TYR 0.013 0.001 TYR A 305 ARG 0.005 0.000 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4378 Ramachandran restraints generated. 2189 Oldfield, 0 Emsley, 2189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4378 Ramachandran restraints generated. 2189 Oldfield, 0 Emsley, 2189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 251 time to evaluate : 2.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 GLN cc_start: 0.8482 (mt0) cc_final: 0.8213 (mt0) REVERT: A 285 MET cc_start: 0.8296 (ptm) cc_final: 0.8031 (ptm) REVERT: A 523 MET cc_start: 0.8638 (mtt) cc_final: 0.8397 (mtt) REVERT: B 92 MET cc_start: 0.8193 (mmm) cc_final: 0.7366 (mmp) REVERT: B 179 MET cc_start: 0.7799 (tpt) cc_final: 0.7231 (tpt) REVERT: B 523 MET cc_start: 0.7806 (tpt) cc_final: 0.7558 (tpt) REVERT: B 744 MET cc_start: 0.8195 (mmm) cc_final: 0.7922 (mmm) REVERT: C 628 GLN cc_start: 0.6895 (mm110) cc_final: 0.6642 (mm-40) REVERT: C 648 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8442 (mt) outliers start: 15 outliers final: 13 residues processed: 257 average time/residue: 0.9406 time to fit residues: 339.4925 Evaluate side-chains 259 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 245 time to evaluate : 2.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 300 GLN Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 648 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 19 optimal weight: 20.0000 chunk 166 optimal weight: 0.8980 chunk 192 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18703 Z= 0.267 Angle : 0.518 4.707 25368 Z= 0.276 Chirality : 0.040 0.164 2815 Planarity : 0.004 0.048 3163 Dihedral : 11.202 174.055 2864 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.97 % Allowed : 11.23 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.17), residues: 2189 helix: 0.59 (0.17), residues: 950 sheet: -0.94 (0.30), residues: 278 loop : -1.70 (0.18), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 438 HIS 0.003 0.001 HIS C 357 PHE 0.014 0.001 PHE A 520 TYR 0.011 0.001 TYR B 559 ARG 0.006 0.000 ARG B 707 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4378 Ramachandran restraints generated. 2189 Oldfield, 0 Emsley, 2189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4378 Ramachandran restraints generated. 2189 Oldfield, 0 Emsley, 2189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 246 time to evaluate : 2.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 GLN cc_start: 0.8505 (mt0) cc_final: 0.8228 (mt0) REVERT: A 285 MET cc_start: 0.8358 (ptm) cc_final: 0.8125 (ptm) REVERT: A 523 MET cc_start: 0.8658 (mtt) cc_final: 0.8433 (mtt) REVERT: B 179 MET cc_start: 0.7872 (tpt) cc_final: 0.7302 (tpt) REVERT: B 523 MET cc_start: 0.7893 (tpt) cc_final: 0.7679 (tpt) REVERT: B 744 MET cc_start: 0.8274 (mmm) cc_final: 0.7967 (mmm) REVERT: C 51 MET cc_start: 0.8871 (mmp) cc_final: 0.8470 (mmp) REVERT: C 300 GLN cc_start: 0.6845 (OUTLIER) cc_final: 0.6517 (mp10) REVERT: C 628 GLN cc_start: 0.6913 (mm110) cc_final: 0.6659 (mm-40) REVERT: C 648 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8481 (mt) outliers start: 19 outliers final: 15 residues processed: 253 average time/residue: 0.8991 time to fit residues: 316.5627 Evaluate side-chains 260 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 243 time to evaluate : 3.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 300 GLN Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain C residue 648 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 203 optimal weight: 2.9990 chunk 185 optimal weight: 6.9990 chunk 197 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 178 optimal weight: 0.9980 chunk 186 optimal weight: 4.9990 chunk 196 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 18703 Z= 0.330 Angle : 0.560 5.409 25368 Z= 0.299 Chirality : 0.042 0.170 2815 Planarity : 0.005 0.045 3163 Dihedral : 11.328 172.871 2864 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.13 % Allowed : 11.28 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.17), residues: 2189 helix: 0.43 (0.17), residues: 948 sheet: -0.95 (0.30), residues: 279 loop : -1.73 (0.18), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 368 HIS 0.006 0.001 HIS A 74 PHE 0.016 0.002 PHE A 520 TYR 0.010 0.002 TYR B 559 ARG 0.004 0.000 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4378 Ramachandran restraints generated. 2189 Oldfield, 0 Emsley, 2189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4378 Ramachandran restraints generated. 2189 Oldfield, 0 Emsley, 2189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 245 time to evaluate : 2.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 GLN cc_start: 0.8491 (mt0) cc_final: 0.8229 (mt0) REVERT: A 523 MET cc_start: 0.8705 (mtt) cc_final: 0.8480 (mtt) REVERT: B 179 MET cc_start: 0.7953 (tpt) cc_final: 0.7402 (tpt) REVERT: B 638 GLU cc_start: 0.6435 (mm-30) cc_final: 0.6087 (mm-30) REVERT: B 706 ARG cc_start: 0.7801 (mmm-85) cc_final: 0.7252 (mtm-85) REVERT: B 744 MET cc_start: 0.8346 (mmm) cc_final: 0.8017 (mmm) REVERT: C 51 MET cc_start: 0.8858 (mmp) cc_final: 0.8434 (mmp) REVERT: C 65 GLU cc_start: 0.7536 (pt0) cc_final: 0.7281 (pt0) REVERT: C 300 GLN cc_start: 0.6864 (OUTLIER) cc_final: 0.6452 (mp10) REVERT: C 628 GLN cc_start: 0.6939 (mm110) cc_final: 0.6676 (mm-40) REVERT: C 648 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8496 (mt) outliers start: 22 outliers final: 18 residues processed: 256 average time/residue: 0.9124 time to fit residues: 325.5147 Evaluate side-chains 260 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 240 time to evaluate : 2.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 300 GLN Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain C residue 648 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 208 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 chunk 201 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 134 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 18703 Z= 0.241 Angle : 0.516 6.017 25368 Z= 0.275 Chirality : 0.040 0.167 2815 Planarity : 0.004 0.042 3163 Dihedral : 11.246 172.555 2864 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.82 % Allowed : 11.74 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.17), residues: 2189 helix: 0.50 (0.17), residues: 953 sheet: -0.89 (0.30), residues: 279 loop : -1.65 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 368 HIS 0.004 0.001 HIS A 326 PHE 0.013 0.001 PHE A 520 TYR 0.010 0.001 TYR B 559 ARG 0.004 0.000 ARG A 204 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4378 Ramachandran restraints generated. 2189 Oldfield, 0 Emsley, 2189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4378 Ramachandran restraints generated. 2189 Oldfield, 0 Emsley, 2189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 238 time to evaluate : 2.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 GLN cc_start: 0.8485 (mt0) cc_final: 0.8228 (mt0) REVERT: A 523 MET cc_start: 0.8650 (mtt) cc_final: 0.8424 (mtt) REVERT: B 179 MET cc_start: 0.7960 (tpt) cc_final: 0.7410 (tpt) REVERT: B 638 GLU cc_start: 0.6394 (mm-30) cc_final: 0.6074 (mm-30) REVERT: B 706 ARG cc_start: 0.7785 (mmm-85) cc_final: 0.7250 (mtm-85) REVERT: B 744 MET cc_start: 0.8223 (mmm) cc_final: 0.7929 (mmm) REVERT: C 51 MET cc_start: 0.8843 (mmp) cc_final: 0.8438 (mmp) REVERT: C 65 GLU cc_start: 0.7520 (pt0) cc_final: 0.7258 (pt0) REVERT: C 300 GLN cc_start: 0.6839 (OUTLIER) cc_final: 0.6442 (mp10) REVERT: C 628 GLN cc_start: 0.6997 (mm110) cc_final: 0.6760 (mm-40) REVERT: C 648 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8520 (mt) outliers start: 16 outliers final: 12 residues processed: 245 average time/residue: 0.9489 time to fit residues: 320.1607 Evaluate side-chains 251 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 237 time to evaluate : 2.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 300 GLN Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain C residue 648 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 160 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 174 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 179 optimal weight: 4.9990 chunk 22 optimal weight: 0.0970 chunk 32 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.148291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.116195 restraints weight = 60319.849| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.61 r_work: 0.3040 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 18703 Z= 0.145 Angle : 0.465 4.875 25368 Z= 0.247 Chirality : 0.038 0.157 2815 Planarity : 0.004 0.039 3163 Dihedral : 11.072 173.057 2864 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.62 % Allowed : 12.05 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.18), residues: 2189 helix: 0.79 (0.17), residues: 954 sheet: -0.70 (0.31), residues: 277 loop : -1.54 (0.19), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 368 HIS 0.004 0.001 HIS A 326 PHE 0.011 0.001 PHE B 185 TYR 0.008 0.001 TYR C 360 ARG 0.007 0.000 ARG A 204 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8387.45 seconds wall clock time: 149 minutes 28.47 seconds (8968.47 seconds total)