Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 17 22:49:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rr7_4986/10_2023/6rr7_4986_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rr7_4986/10_2023/6rr7_4986.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rr7_4986/10_2023/6rr7_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_4986/10_2023/6rr7_4986_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rr7_4986/10_2023/6rr7_4986_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rr7_4986/10_2023/6rr7_4986.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rr7_4986/10_2023/6rr7_4986.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rr7_4986/10_2023/6rr7_4986_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rr7_4986/10_2023/6rr7_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-1.21rc1-5097/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: 15.58, per 1000 atoms: 0.43 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: 28.84 Conformation dependent library (CDL) restraints added in 3.0 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: 18.39 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: 14.83 Time building geometry restraints manager: 29.61 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: 14375 34.80 - 69.59: 354 69.59 - 104.39: 25 104.39 - 139.19: 0 139.19 - 173.99: 2 Dihedral angle restraints: 14756 sinusoidal: 7322 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 14753 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: 0.940 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: 0.490 Extract box with map and model: 5.040 Check model and map are aligned: 0.510 Set scattering table: 0.310 Process input model: 121.820 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.100 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: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.030 ------------------------------------------------------------------------------- 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 : 15.019 173.986 7239 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 *********************** 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 : 2.857 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 outliers start: 0 outliers final: 0 residues processed: 371 average time/residue: 1.0148 time to fit residues: 513.1970 Evaluate side-chains 271 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 3.057 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9132 ------------------------------------------------------------------------------- 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: 2.9990 chunk 166 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 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: 0.7980 chunk 199 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7888 moved from start: 0.1696 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= 0.167 Angle : 0.541 5.967 25368 Z= 0.285 Chirality : 0.039 0.173 2815 Planarity : 0.004 0.059 3163 Dihedral : 8.659 174.720 2760 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.56 % Allowed : 7.23 % Favored : 92.21 % 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: -2.37 (0.16), residues: 2189 helix: -0.52 (0.16), residues: 931 sheet: -1.87 (0.28), residues: 274 loop : -2.52 (0.17), residues: 984 *********************** 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 289 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 278 time to evaluate : 2.943 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 outliers start: 11 outliers final: 8 residues processed: 283 average time/residue: 0.9160 time to fit residues: 367.4678 Evaluate side-chains 273 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 265 time to evaluate : 2.775 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.4266 time to fit residues: 9.9011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0470 chunk 166 optimal weight: 0.0070 chunk 136 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 200 optimal weight: 3.9990 chunk 216 optimal weight: 7.9990 chunk 178 optimal weight: 5.9990 chunk 198 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 overall best weight: 1.8102 ------------------------------------------------------------------------------- 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: 0.7975 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18703 Z= 0.274 Angle : 0.554 4.962 25368 Z= 0.293 Chirality : 0.041 0.177 2815 Planarity : 0.004 0.054 3163 Dihedral : 8.613 174.849 2760 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.51 % Allowed : 8.62 % Favored : 90.87 % 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: -1.76 (0.17), residues: 2189 helix: -0.02 (0.17), residues: 937 sheet: -1.49 (0.30), residues: 276 loop : -2.23 (0.18), residues: 976 *********************** 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 274 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 264 time to evaluate : 3.111 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 outliers start: 10 outliers final: 6 residues processed: 270 average time/residue: 0.9349 time to fit residues: 354.9354 Evaluate side-chains 257 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 251 time to evaluate : 2.694 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3839 time to fit residues: 8.0713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 103 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 134 optimal weight: 0.0980 chunk 200 optimal weight: 3.9990 chunk 212 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 190 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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** C 540 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2602 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= 0.199 Angle : 0.504 5.938 25368 Z= 0.266 Chirality : 0.039 0.178 2815 Planarity : 0.004 0.046 3163 Dihedral : 8.396 175.238 2760 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.36 % Allowed : 9.74 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.17), residues: 2189 helix: 0.37 (0.17), residues: 943 sheet: -1.23 (0.30), residues: 276 loop : -1.97 (0.18), residues: 970 *********************** 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 265 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 258 time to evaluate : 2.949 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 outliers start: 7 outliers final: 5 residues processed: 260 average time/residue: 0.9149 time to fit residues: 334.6914 Evaluate side-chains 253 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 248 time to evaluate : 2.732 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.4025 time to fit residues: 7.3775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 177 optimal weight: 3.9990 chunk 120 optimal weight: 0.0870 chunk 3 optimal weight: 9.9990 chunk 158 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 181 optimal weight: 6.9990 chunk 146 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 190 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- 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 A 248 GLN ** 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: 0.7989 moved from start: 0.2845 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= 0.229 Angle : 0.516 5.680 25368 Z= 0.273 Chirality : 0.040 0.173 2815 Planarity : 0.004 0.049 3163 Dihedral : 8.345 174.772 2760 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.26 % Allowed : 10.97 % Favored : 88.77 % 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: -1.13 (0.17), residues: 2189 helix: 0.48 (0.17), residues: 944 sheet: -1.14 (0.30), residues: 276 loop : -1.88 (0.18), residues: 969 *********************** 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 258 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 253 time to evaluate : 3.069 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 outliers start: 5 outliers final: 3 residues processed: 255 average time/residue: 0.9052 time to fit residues: 323.6595 Evaluate side-chains 253 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 250 time to evaluate : 3.038 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.5180 time to fit residues: 6.5637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 42 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 212 optimal weight: 5.9990 chunk 176 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 17 optimal weight: 9.9990 chunk 70 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 248 GLN ** 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: 0.7975 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18703 Z= 0.185 Angle : 0.485 5.618 25368 Z= 0.257 Chirality : 0.039 0.167 2815 Planarity : 0.004 0.051 3163 Dihedral : 8.238 174.922 2760 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.41 % Allowed : 11.23 % Favored : 88.36 % 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: -0.91 (0.18), residues: 2189 helix: 0.64 (0.17), residues: 950 sheet: -0.97 (0.30), residues: 276 loop : -1.77 (0.18), residues: 963 *********************** 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 263 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 255 time to evaluate : 2.979 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 outliers start: 8 outliers final: 8 residues processed: 257 average time/residue: 0.9259 time to fit residues: 334.5909 Evaluate side-chains 257 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 249 time to evaluate : 3.087 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3874 time to fit residues: 9.5301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 120 optimal weight: 0.0870 chunk 179 optimal weight: 9.9990 chunk 118 optimal weight: 2.9990 chunk 212 optimal weight: 5.9990 chunk 132 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 97 optimal weight: 0.0170 overall best weight: 0.9398 ------------------------------------------------------------------------------- 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: 0.7966 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 18703 Z= 0.161 Angle : 0.471 5.129 25368 Z= 0.249 Chirality : 0.038 0.157 2815 Planarity : 0.003 0.042 3163 Dihedral : 8.139 175.049 2760 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.05 % Allowed : 11.54 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.18), residues: 2189 helix: 0.81 (0.17), residues: 949 sheet: -0.87 (0.30), residues: 276 loop : -1.68 (0.18), residues: 964 *********************** 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 257 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 256 time to evaluate : 2.821 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 outliers start: 1 outliers final: 1 residues processed: 256 average time/residue: 0.8988 time to fit residues: 322.6170 Evaluate side-chains 249 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 248 time to evaluate : 2.568 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4833 time to fit residues: 4.4411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 0.6980 chunk 84 optimal weight: 0.1980 chunk 126 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 166 optimal weight: 0.8980 chunk 192 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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: 0.7981 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18703 Z= 0.197 Angle : 0.489 6.844 25368 Z= 0.259 Chirality : 0.039 0.159 2815 Planarity : 0.004 0.043 3163 Dihedral : 8.147 174.767 2760 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.26 % Allowed : 11.79 % Favored : 87.95 % 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: -0.69 (0.18), residues: 2189 helix: 0.82 (0.17), residues: 947 sheet: -0.86 (0.30), residues: 278 loop : -1.64 (0.18), residues: 964 *********************** 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 252 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 247 time to evaluate : 3.074 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 outliers start: 5 outliers final: 4 residues processed: 248 average time/residue: 0.9496 time to fit residues: 329.3823 Evaluate side-chains 248 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 244 time to evaluate : 2.755 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3925 time to fit residues: 6.6015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 203 optimal weight: 0.0170 chunk 185 optimal weight: 6.9990 chunk 197 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 chunk 196 optimal weight: 0.1980 chunk 129 optimal weight: 0.8980 overall best weight: 1.2222 ------------------------------------------------------------------------------- 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 A 248 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18703 Z= 0.180 Angle : 0.477 4.872 25368 Z= 0.252 Chirality : 0.038 0.160 2815 Planarity : 0.003 0.039 3163 Dihedral : 8.113 174.709 2760 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % 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: -0.58 (0.18), residues: 2189 helix: 0.89 (0.17), residues: 947 sheet: -0.77 (0.31), residues: 278 loop : -1.56 (0.18), residues: 964 *********************** 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 248 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 2.870 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 outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.9059 time to fit residues: 313.5234 Evaluate side-chains 245 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 2.742 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 208 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 chunk 201 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18703 Z= 0.282 Angle : 0.528 6.495 25368 Z= 0.280 Chirality : 0.041 0.307 2815 Planarity : 0.004 0.040 3163 Dihedral : 8.222 173.839 2760 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.21 % Allowed : 12.15 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.18), residues: 2189 helix: 0.71 (0.17), residues: 948 sheet: -0.81 (0.31), residues: 279 loop : -1.59 (0.18), residues: 962 ********************** 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 250 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 246 time to evaluate : 3.156 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 outliers start: 4 outliers final: 4 residues processed: 247 average time/residue: 0.9123 time to fit residues: 314.9090 Evaluate side-chains 246 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 242 time to evaluate : 2.734 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4265 time to fit residues: 6.8435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 160 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 chunk 73 optimal weight: 0.0980 chunk 179 optimal weight: 6.9990 chunk 22 optimal weight: 0.0980 chunk 32 optimal weight: 0.9980 chunk 153 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3692 r_free = 0.3692 target = 0.150536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.118048 restraints weight = 59844.192| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.56 r_work: 0.3052 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 18703 Z= 0.129 Angle : 0.463 5.658 25368 Z= 0.245 Chirality : 0.038 0.207 2815 Planarity : 0.003 0.036 3163 Dihedral : 8.053 174.464 2760 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.05 % Allowed : 12.21 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.18), residues: 2189 helix: 0.99 (0.17), residues: 952 sheet: -0.64 (0.31), residues: 277 loop : -1.49 (0.19), residues: 960 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8389.06 seconds wall clock time: 149 minutes 12.74 seconds (8952.74 seconds total)