Starting phenix.real_space_refine (version: dev) on Wed Feb 22 22:20:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0v_10360/02_2023/6t0v_10360_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0v_10360/02_2023/6t0v_10360.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0v_10360/02_2023/6t0v_10360_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0v_10360/02_2023/6t0v_10360_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0v_10360/02_2023/6t0v_10360_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0v_10360/02_2023/6t0v_10360.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0v_10360/02_2023/6t0v_10360.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0v_10360/02_2023/6t0v_10360_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0v_10360/02_2023/6t0v_10360_updated.pdb" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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 Process input model Symmetric amino acids flipped Residue "A ARG 266": "NH1" <-> "NH2" Residue "A ARG 279": "NH1" <-> "NH2" Residue "A PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 300": "OE1" <-> "OE2" Residue "A ARG 396": "NH1" <-> "NH2" Residue "A GLU 419": "OE1" <-> "OE2" Residue "A ARG 503": "NH1" <-> "NH2" Residue "A ARG 507": "NH1" <-> "NH2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 533": "OE1" <-> "OE2" Residue "A ARG 608": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "B GLU 90": "OE1" <-> "OE2" Residue "B ARG 97": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 209": "NH1" <-> "NH2" Residue "B ARG 353": "NH1" <-> "NH2" Residue "B ARG 434": "NH1" <-> "NH2" Residue "B ARG 560": "NH1" <-> "NH2" Residue "B ARG 571": "NH1" <-> "NH2" Residue "B PHE 696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 706": "NH1" <-> "NH2" Residue "B ARG 707": "NH1" <-> "NH2" Residue "B ARG 723": "NH1" <-> "NH2" Residue "C ARG 3": "NH1" <-> "NH2" Residue "C ARG 15": "NH1" <-> "NH2" Residue "C TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 427": "NH1" <-> "NH2" Residue "C GLU 662": "OE1" <-> "OE2" Residue "C GLU 682": "OE1" <-> "OE2" Residue "C ARG 737": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 18604 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 705, 5746 Classifications: {'peptide': 705} Link IDs: {'PTRANS': 25, 'TRANS': 679} Chain breaks: 2 Chain: "B" Number of atoms: 5950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5950 Classifications: {'peptide': 745} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 716} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 5878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5878 Classifications: {'peptide': 740} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 30, 'TRANS': 709} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "V" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 307 Classifications: {'RNA': 14} Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 2} Link IDs: {'rna2p': 4, 'rna3p': 9} Chain: "R" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 367 Classifications: {'RNA': 18} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 6, 'rna3p_pur': 3, 'rna3p_pyr': 8} Link IDs: {'rna2p': 7, 'rna3p': 10} Chain: "M" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 296 Unusual residues: {'GTG': 1} Classifications: {'RNA': 11, 'undetermined': 1} Modifications used: {'rna3p_pur': 10, 'rna3p_pyr': 1} Link IDs: {'rna3p': 10, None: 1} Not linked: pdbres="GTG M 1 " pdbres=" A M 2 " Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Unusual residues: {' MG': 2, 'M4H': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 32 Unusual residues: {' MG': 3, '2KH': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 11.68, per 1000 atoms: 0.63 Number of scatterers: 18604 At special positions: 0 Unit cell: (120.28, 127.594, 116.216, 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 108 16.00 P 48 15.00 Mg 5 11.99 O 3628 8.00 N 3253 7.00 C 11562 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.10 Conformation dependent library (CDL) restraints added in 2.9 seconds 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4116 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 82 helices and 20 sheets defined 40.0% alpha, 12.1% beta 11 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 6.72 Creating SS restraints... Processing helix chain 'A' and resid 2 through 5 No H-bonds generated for 'chain 'A' and resid 2 through 5' Processing helix chain 'A' and resid 11 through 24 removed outlier: 3.908A pdb=" N TYR A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 49 removed outlier: 3.556A pdb=" N ALA A 36 " --> pdb=" O GLY A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 95 Processing helix chain 'A' and resid 127 through 137 Processing helix chain 'A' and resid 165 through 182 Processing helix chain 'A' and resid 188 through 193 Processing helix chain 'A' and resid 209 through 218 removed outlier: 3.575A pdb=" N SER A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 234 Processing helix chain 'A' and resid 241 through 248 Processing helix chain 'A' and resid 303 through 313 removed outlier: 3.964A pdb=" N THR A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 346 Processing helix chain 'A' and resid 359 through 364 Processing helix chain 'A' and resid 376 through 378 No H-bonds generated for 'chain 'A' and resid 376 through 378' Processing helix chain 'A' and resid 401 through 409 Processing helix chain 'A' and resid 429 through 445 Processing helix chain 'A' and resid 449 through 470 Processing helix chain 'A' and resid 525 through 527 No H-bonds generated for 'chain 'A' and resid 525 through 527' Processing helix chain 'A' and resid 529 through 532 Processing helix chain 'A' and resid 567 through 574 Processing helix chain 'A' and resid 576 through 598 removed outlier: 3.633A pdb=" N SER A 583 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU A 584 " --> pdb=" O LEU A 581 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLN A 585 " --> pdb=" O GLN A 582 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL A 587 " --> pdb=" O LEU A 584 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA A 593 " --> pdb=" O MET A 590 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA A 596 " --> pdb=" O ALA A 593 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS A 598 " --> pdb=" O SER A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 608 Processing helix chain 'A' and resid 628 through 644 Processing helix chain 'A' and resid 648 through 668 removed outlier: 4.096A pdb=" N LYS A 659 " --> pdb=" O ALA A 655 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 686 Processing helix chain 'A' and resid 693 through 712 Processing helix chain 'B' and resid 5 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 removed outlier: 3.596A pdb=" N GLN B 115 " --> pdb=" O ILE B 111 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN B 116 " --> pdb=" O ASP B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 123 Processing helix chain 'B' and resid 139 through 152 Processing helix chain 'B' and resid 157 through 160 Processing helix chain 'B' and resid 163 through 175 removed outlier: 3.961A pdb=" N PHE B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N GLU B 175 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 221 Processing helix chain 'B' and resid 246 through 265 removed outlier: 4.263A pdb=" N GLY B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG B 265 " --> pdb=" O ASN 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 345 removed outlier: 4.709A pdb=" N ALA B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 383 through 395 removed outlier: 5.500A pdb=" N HIS B 394 " --> pdb=" O GLU B 390 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU B 395 " --> pdb=" O LYS B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 427 removed outlier: 3.740A pdb=" N VAL B 423 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY B 427 " --> pdb=" O VAL B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 432 No H-bonds generated for 'chain 'B' and resid 429 through 432' Processing helix chain 'B' and resid 456 through 473 removed outlier: 3.654A pdb=" N VAL B 473 " --> pdb=" O THR B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 511 Proline residue: B 510 - end of helix Processing helix chain 'B' and resid 519 through 535 removed outlier: 3.847A pdb=" N MET B 523 " --> pdb=" O GLU B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 559 Processing helix chain 'B' and resid 573 through 581 Processing helix chain 'B' and resid 586 through 588 No H-bonds generated for 'chain 'B' and resid 586 through 588' Processing helix chain 'B' and resid 591 through 593 No H-bonds generated for 'chain 'B' and resid 591 through 593' Processing helix chain 'B' and resid 608 through 611 No H-bonds generated for 'chain 'B' and resid 608 through 611' Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 684 through 697 Processing helix chain 'B' and resid 701 through 703 No H-bonds generated for 'chain 'B' and resid 701 through 703' Processing helix chain 'B' and resid 714 through 732 Processing helix chain 'B' and resid 737 through 753 Processing helix chain 'C' and resid 2 through 12 removed outlier: 3.684A pdb=" N LYS C 12 " --> pdb=" O MET C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 22 Processing helix chain 'C' and resid 27 through 29 No H-bonds generated for 'chain 'C' and resid 27 through 29' Processing helix chain 'C' and resid 43 through 52 removed outlier: 3.546A pdb=" N MET C 51 " --> pdb=" O MET C 47 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ALA C 52 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 66 removed outlier: 3.632A pdb=" N MET C 66 " --> pdb=" O ILE C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 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 156 through 166 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: 4.149A pdb=" N GLN C 257 " --> pdb=" O ASP C 253 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL C 272 " --> pdb=" O ARG C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 286 removed outlier: 3.729A pdb=" N HIS C 285 " --> pdb=" O LEU C 281 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR C 286 " --> pdb=" O SER C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 297 No H-bonds generated for 'chain 'C' and resid 294 through 297' Processing helix chain 'C' and resid 308 through 315 Processing helix chain 'C' and resid 391 through 404 removed outlier: 3.559A pdb=" N LEU C 395 " --> pdb=" O LEU C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 440 removed outlier: 3.909A pdb=" N LYS C 440 " --> pdb=" O ARG C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 449 Processing helix chain 'C' and resid 515 through 517 No H-bonds generated for 'chain 'C' and resid 515 through 517' Processing helix chain 'C' and resid 542 through 555 Processing helix chain 'C' and resid 557 through 565 removed outlier: 3.697A pdb=" N THR C 562 " --> pdb=" O GLU C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 577 No H-bonds generated for 'chain 'C' and resid 575 through 577' Processing helix chain 'C' and resid 588 through 605 Processing helix chain 'C' and resid 612 through 621 removed outlier: 3.860A pdb=" N LEU C 618 " --> pdb=" O GLN C 614 " (cutoff:3.500A) Proline residue: C 620 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 109 through 111 Processing sheet with id= B, first strand: chain 'A' and resid 290 through 293 removed outlier: 6.377A pdb=" N ILE A 480 " --> pdb=" O TYR A 496 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N PHE A 498 " --> pdb=" O ILE A 478 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE A 478 " --> pdb=" O PHE A 498 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 497 through 501 removed outlier: 6.421A pdb=" N LEU A 558 " --> pdb=" O GLU A 539 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N GLU A 539 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL A 560 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N VAL A 537 " --> pdb=" O VAL A 560 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N GLU A 539 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ILE A 322 " --> pdb=" O GLU A 539 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 614 through 618 removed outlier: 6.689A pdb=" N GLU A 624 " --> pdb=" O ILE A 616 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 54 through 57 Processing sheet with id= F, first strand: chain 'B' and resid 128 through 130 Processing sheet with id= G, first strand: chain 'B' and resid 180 through 192 removed outlier: 3.513A pdb=" N VAL B 210 " --> pdb=" O VAL B 181 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 240 through 243 removed outlier: 6.691A pdb=" N VAL B 348 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N THR B 226 " --> pdb=" O VAL B 348 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ARG B 350 " --> pdb=" O THR B 226 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N THR B 228 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 483 through 486 removed outlier: 3.500A pdb=" N PHE B 447 " --> pdb=" O GLY B 304 " (cutoff:3.500A) 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 491 Processing sheet with id= L, first strand: chain 'C' and resid 57 through 60 Processing sheet with id= M, first strand: chain 'C' and resid 133 through 135 Processing sheet with id= N, first strand: chain 'C' and resid 287 through 289 Processing sheet with id= O, first strand: chain 'C' and resid 323 through 325 removed outlier: 3.718A pdb=" N PHE C 323 " --> pdb=" O PHE C 330 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLU C 362 " --> pdb=" O VAL C 333 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL C 373 " --> pdb=" O ILE C 385 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN C 383 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N GLY C 377 " --> pdb=" O LEU C 381 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N LEU C 381 " --> pdb=" O GLY C 377 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 338 through 345 Processing sheet with id= Q, first strand: chain 'C' and resid 635 through 640 Processing sheet with id= R, first strand: chain 'C' and resid 656 through 659 removed outlier: 3.818A pdb=" N GLY C 673 " --> pdb=" O ILE C 665 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N VAL C 667 " --> pdb=" O SER C 671 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N SER C 671 " --> pdb=" O VAL C 667 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 694 through 696 removed outlier: 4.263A pdb=" N GLY C 727 " --> pdb=" O ASP C 730 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N VAL C 732 " --> pdb=" O LEU C 725 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N LEU C 725 " --> pdb=" O VAL C 732 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL C 734 " --> pdb=" O ASN C 723 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ASN C 723 " --> pdb=" O VAL C 734 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 141 through 148 removed outlier: 6.349A pdb=" N ARG C 214 " --> pdb=" O ILE C 147 " (cutoff:3.500A) 671 hydrogen bonds defined for protein. 1881 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 54 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 6.28 Time building geometry restraints manager: 7.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3005 1.31 - 1.43: 5221 1.43 - 1.56: 10544 1.56 - 1.69: 92 1.69 - 1.81: 191 Bond restraints: 19053 Sorted by residual: bond pdb=" C3D GTG M 1 " pdb=" C4D GTG M 1 " ideal model delta sigma weight residual 1.298 1.550 -0.252 2.00e-02 2.50e+03 1.59e+02 bond pdb=" C2E GTG M 1 " pdb=" C3E GTG M 1 " ideal model delta sigma weight residual 1.254 1.494 -0.240 2.00e-02 2.50e+03 1.44e+02 bond pdb=" C1' 2KH B 801 " pdb=" O4' 2KH B 801 " ideal model delta sigma weight residual 1.561 1.321 0.240 2.00e-02 2.50e+03 1.44e+02 bond pdb=" C4' 2KH B 801 " pdb=" O4' 2KH B 801 " ideal model delta sigma weight residual 1.310 1.532 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C5B GTG M 1 " pdb=" C6B GTG M 1 " ideal model delta sigma weight residual 1.538 1.325 0.213 2.00e-02 2.50e+03 1.14e+02 ... (remaining 19048 not shown) Histogram of bond angle deviations from ideal: 95.93 - 104.67: 500 104.67 - 113.41: 10695 113.41 - 122.16: 11168 122.16 - 130.90: 3468 130.90 - 139.64: 93 Bond angle restraints: 25924 Sorted by residual: angle pdb=" C1D GTG M 1 " pdb=" N9A GTG M 1 " pdb=" C4A GTG M 1 " ideal model delta sigma weight residual 93.21 126.25 -33.04 3.00e+00 1.11e-01 1.21e+02 angle pdb=" C1D GTG M 1 " pdb=" N9A GTG M 1 " pdb=" C8A GTG M 1 " ideal model delta sigma weight residual 157.61 125.32 32.29 3.00e+00 1.11e-01 1.16e+02 angle pdb=" C1E GTG M 1 " pdb=" N9B GTG M 1 " pdb=" C4B GTG M 1 " ideal model delta sigma weight residual 152.69 128.62 24.07 3.00e+00 1.11e-01 6.44e+01 angle pdb=" C1E GTG M 1 " pdb=" N9B GTG M 1 " pdb=" C8B GTG M 1 " ideal model delta sigma weight residual 99.21 123.21 -24.00 3.00e+00 1.11e-01 6.40e+01 angle pdb=" N18 M4H A 801 " pdb=" C19 M4H A 801 " pdb=" N26 M4H A 801 " ideal model delta sigma weight residual 125.81 139.64 -13.83 3.00e+00 1.11e-01 2.13e+01 ... (remaining 25919 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.19: 10678 24.19 - 48.39: 625 48.39 - 72.58: 137 72.58 - 96.78: 19 96.78 - 120.97: 1 Dihedral angle restraints: 11460 sinusoidal: 5092 harmonic: 6368 Sorted by residual: dihedral pdb=" CA MET B 409 " pdb=" C MET B 409 " pdb=" N GLY B 410 " pdb=" CA GLY B 410 " ideal model delta harmonic sigma weight residual 180.00 152.86 27.14 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA PHE B 447 " pdb=" C PHE B 447 " pdb=" N ALA B 448 " pdb=" CA ALA B 448 " ideal model delta harmonic sigma weight residual 180.00 154.30 25.70 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA SER C 366 " pdb=" C SER C 366 " pdb=" N GLY C 367 " pdb=" CA GLY C 367 " ideal model delta harmonic sigma weight residual 180.00 159.75 20.25 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 11457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2597 0.081 - 0.162: 274 0.162 - 0.242: 11 0.242 - 0.323: 2 0.323 - 0.404: 1 Chirality restraints: 2885 Sorted by residual: chirality pdb=" C3D GTG M 1 " pdb=" C2D GTG M 1 " pdb=" C4D GTG M 1 " pdb=" O3D GTG M 1 " both_signs ideal model delta sigma weight residual False -2.38 -2.78 0.40 2.00e-01 2.50e+01 4.08e+00 chirality pdb=" C3E GTG M 1 " pdb=" C2E GTG M 1 " pdb=" C4E GTG M 1 " pdb=" O3E GTG M 1 " both_signs ideal model delta sigma weight residual False -2.43 -2.74 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" C2E GTG M 1 " pdb=" C1E GTG M 1 " pdb=" C3E GTG M 1 " pdb=" O2E GTG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 2882 not shown) Planarity restraints: 3163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 329 " 0.045 5.00e-02 4.00e+02 6.83e-02 7.47e+00 pdb=" N PRO B 330 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 330 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 330 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A V 7 " -0.035 2.00e-02 2.50e+03 1.61e-02 7.15e+00 pdb=" N9 A V 7 " 0.038 2.00e-02 2.50e+03 pdb=" C8 A V 7 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A V 7 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A V 7 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A V 7 " -0.005 2.00e-02 2.50e+03 pdb=" N6 A V 7 " -0.009 2.00e-02 2.50e+03 pdb=" N1 A V 7 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A V 7 " 0.004 2.00e-02 2.50e+03 pdb=" N3 A V 7 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A V 7 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 619 " -0.044 5.00e-02 4.00e+02 6.63e-02 7.02e+00 pdb=" N PRO A 620 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 620 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 620 " -0.037 5.00e-02 4.00e+02 ... (remaining 3160 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 136 2.47 - 3.08: 11163 3.08 - 3.68: 28823 3.68 - 4.29: 45599 4.29 - 4.90: 73505 Nonbonded interactions: 159226 Sorted by model distance: nonbonded pdb=" O11 M4H A 801 " pdb="MG MG A 802 " model vdw 1.859 2.170 nonbonded pdb=" OD1 ASP A 108 " pdb="MG MG A 803 " model vdw 1.871 2.170 nonbonded pdb=" OE2 GLU A 119 " pdb="MG MG A 802 " model vdw 1.873 2.170 nonbonded pdb=" OD2 ASP A 108 " pdb="MG MG A 802 " model vdw 1.884 2.170 nonbonded pdb=" O ILE A 120 " pdb="MG MG A 802 " model vdw 1.885 2.170 ... (remaining 159221 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 Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 48 5.49 5 Mg 5 5.21 5 S 108 5.16 5 C 11562 2.51 5 N 3253 2.21 5 O 3628 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.870 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: 0.000 Extract box with map and model: 8.430 Check model and map are aligned: 0.250 Process input model: 53.360 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.170 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 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 : 0.009 0.252 19053 Z= 0.539 Angle : 0.874 33.039 25924 Z= 0.454 Chirality : 0.050 0.404 2885 Planarity : 0.006 0.068 3163 Dihedral : 15.791 120.971 7344 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer Outliers : 7.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -3.31 (0.14), residues: 2178 helix: -2.14 (0.12), residues: 949 sheet: -1.76 (0.28), residues: 247 loop : -2.26 (0.17), residues: 982 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 398 time to evaluate : 2.322 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 143 outliers final: 66 residues processed: 505 average time/residue: 0.3652 time to fit residues: 267.2849 Evaluate side-chains 363 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 297 time to evaluate : 2.054 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 0 residues processed: 66 average time/residue: 0.2044 time to fit residues: 26.6171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 0.6980 chunk 167 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 173 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 200 optimal weight: 8.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 228 GLN A 256 GLN A 403 GLN B 58 ASN B 127 GLN ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN B 452 ASN B 694 GLN C 13 ASN C 39 GLN C 75 ASN C 160 GLN C 182 GLN C 285 HIS C 383 GLN C 524 GLN C 581 GLN C 632 GLN C 657 ASN C 663 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 19053 Z= 0.154 Angle : 0.492 13.520 25924 Z= 0.254 Chirality : 0.039 0.155 2885 Planarity : 0.004 0.049 3163 Dihedral : 7.890 121.359 2906 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 1.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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 (0.16), residues: 2178 helix: -0.37 (0.16), residues: 951 sheet: -1.29 (0.29), residues: 245 loop : -1.78 (0.18), residues: 982 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 320 time to evaluate : 2.034 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 14 residues processed: 342 average time/residue: 0.3765 time to fit residues: 185.2785 Evaluate side-chains 287 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 273 time to evaluate : 2.193 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2466 time to fit residues: 8.8583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 111 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 167 optimal weight: 10.0000 chunk 136 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 chunk 201 optimal weight: 4.9990 chunk 217 optimal weight: 8.9990 chunk 179 optimal weight: 10.0000 chunk 199 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 161 optimal weight: 0.6980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN A 228 GLN B 65 GLN ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 694 GLN C 13 ASN C 524 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 19053 Z= 0.223 Angle : 0.511 13.102 25924 Z= 0.263 Chirality : 0.040 0.147 2885 Planarity : 0.004 0.048 3163 Dihedral : 7.915 115.349 2906 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer Outliers : 2.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -1.07 (0.17), residues: 2178 helix: 0.27 (0.17), residues: 950 sheet: -1.03 (0.31), residues: 245 loop : -1.59 (0.18), residues: 983 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 286 time to evaluate : 2.120 Fit side-chains outliers start: 50 outliers final: 28 residues processed: 319 average time/residue: 0.3613 time to fit residues: 169.7859 Evaluate side-chains 299 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 271 time to evaluate : 1.879 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.1850 time to fit residues: 12.6015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 198 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 95 optimal weight: 0.9980 chunk 135 optimal weight: 10.0000 chunk 201 optimal weight: 4.9990 chunk 213 optimal weight: 4.9990 chunk 105 optimal weight: 9.9990 chunk 191 optimal weight: 20.0000 chunk 57 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 679 GLN C 429 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 19053 Z= 0.306 Angle : 0.557 13.258 25924 Z= 0.286 Chirality : 0.042 0.161 2885 Planarity : 0.004 0.042 3163 Dihedral : 8.128 110.436 2906 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer Outliers : 2.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -0.85 (0.17), residues: 2178 helix: 0.40 (0.17), residues: 951 sheet: -0.72 (0.30), residues: 261 loop : -1.47 (0.19), residues: 966 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 282 time to evaluate : 1.981 Fit side-chains outliers start: 52 outliers final: 27 residues processed: 316 average time/residue: 0.3586 time to fit residues: 166.4473 Evaluate side-chains 286 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 259 time to evaluate : 2.118 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.1824 time to fit residues: 12.1930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 177 optimal weight: 3.9990 chunk 121 optimal weight: 0.0020 chunk 3 optimal weight: 9.9990 chunk 159 optimal weight: 8.9990 chunk 88 optimal weight: 9.9990 chunk 182 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 191 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 overall best weight: 4.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 527 ASN ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 694 GLN C 522 GLN ** C 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 657 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.078 19053 Z= 0.397 Angle : 0.612 13.282 25924 Z= 0.315 Chirality : 0.045 0.198 2885 Planarity : 0.005 0.047 3163 Dihedral : 8.428 108.012 2906 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer Outliers : 2.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.17), residues: 2178 helix: 0.27 (0.17), residues: 955 sheet: -0.86 (0.30), residues: 256 loop : -1.48 (0.19), residues: 967 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 268 time to evaluate : 2.226 Fit side-chains outliers start: 47 outliers final: 25 residues processed: 301 average time/residue: 0.3545 time to fit residues: 158.3951 Evaluate side-chains 284 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 259 time to evaluate : 2.032 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.2003 time to fit residues: 11.8510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 71 optimal weight: 1.9990 chunk 192 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 52 optimal weight: 0.3980 chunk 213 optimal weight: 8.9990 chunk 177 optimal weight: 9.9990 chunk 99 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN C 348 ASN C 654 GLN C 657 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 19053 Z= 0.162 Angle : 0.483 14.470 25924 Z= 0.248 Chirality : 0.039 0.154 2885 Planarity : 0.004 0.070 3163 Dihedral : 8.019 123.900 2906 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -0.46 (0.18), residues: 2178 helix: 0.77 (0.17), residues: 953 sheet: -0.55 (0.31), residues: 254 loop : -1.31 (0.19), residues: 971 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 289 time to evaluate : 2.248 Fit side-chains outliers start: 14 outliers final: 4 residues processed: 296 average time/residue: 0.3640 time to fit residues: 158.8729 Evaluate side-chains 274 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 270 time to evaluate : 2.112 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1942 time to fit residues: 4.4041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 206 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 121 optimal weight: 9.9990 chunk 156 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 179 optimal weight: 6.9990 chunk 119 optimal weight: 2.9990 chunk 213 optimal weight: 20.0000 chunk 133 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 19053 Z= 0.306 Angle : 0.562 13.378 25924 Z= 0.287 Chirality : 0.042 0.166 2885 Planarity : 0.004 0.056 3163 Dihedral : 8.212 116.580 2906 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: 2178 helix: 0.61 (0.17), residues: 953 sheet: -0.47 (0.32), residues: 249 loop : -1.34 (0.19), residues: 976 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 266 time to evaluate : 2.208 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 12 residues processed: 275 average time/residue: 0.3669 time to fit residues: 148.3705 Evaluate side-chains 271 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 259 time to evaluate : 2.278 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2236 time to fit residues: 7.4305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 131 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 41 optimal weight: 0.0770 chunk 135 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 167 optimal weight: 5.9990 chunk 193 optimal weight: 5.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 19053 Z= 0.218 Angle : 0.513 14.044 25924 Z= 0.263 Chirality : 0.040 0.158 2885 Planarity : 0.004 0.047 3163 Dihedral : 8.063 118.840 2906 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -0.40 (0.18), residues: 2178 helix: 0.78 (0.17), residues: 950 sheet: -0.49 (0.31), residues: 254 loop : -1.23 (0.19), residues: 974 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 260 time to evaluate : 2.340 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 265 average time/residue: 0.3775 time to fit residues: 147.5022 Evaluate side-chains 261 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 254 time to evaluate : 2.132 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1846 time to fit residues: 5.4820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 204 optimal weight: 8.9990 chunk 186 optimal weight: 9.9990 chunk 198 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 155 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 chunk 187 optimal weight: 0.9980 chunk 197 optimal weight: 2.9990 chunk 130 optimal weight: 0.0770 overall best weight: 1.5742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 19053 Z= 0.174 Angle : 0.486 14.206 25924 Z= 0.248 Chirality : 0.039 0.162 2885 Planarity : 0.004 0.045 3163 Dihedral : 7.858 119.917 2906 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -0.18 (0.18), residues: 2178 helix: 1.00 (0.17), residues: 942 sheet: -0.35 (0.31), residues: 258 loop : -1.16 (0.20), residues: 978 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 266 time to evaluate : 2.300 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 274 average time/residue: 0.3875 time to fit residues: 155.7486 Evaluate side-chains 263 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 257 time to evaluate : 2.285 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1800 time to fit residues: 5.1038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 209 optimal weight: 6.9990 chunk 128 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 145 optimal weight: 0.6980 chunk 220 optimal weight: 10.0000 chunk 202 optimal weight: 6.9990 chunk 175 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 107 optimal weight: 0.0000 chunk 139 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 19053 Z= 0.172 Angle : 0.502 13.903 25924 Z= 0.254 Chirality : 0.039 0.160 2885 Planarity : 0.004 0.045 3163 Dihedral : 7.824 119.873 2906 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -0.09 (0.18), residues: 2178 helix: 1.08 (0.17), residues: 943 sheet: -0.26 (0.33), residues: 246 loop : -1.11 (0.19), residues: 989 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 262 time to evaluate : 2.328 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 263 average time/residue: 0.3860 time to fit residues: 147.7840 Evaluate side-chains 263 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 258 time to evaluate : 2.132 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2046 time to fit residues: 4.7963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 175 optimal weight: 0.9980 chunk 73 optimal weight: 9.9990 chunk 180 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 154 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 657 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.162225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.138907 restraints weight = 23321.077| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.35 r_work: 0.3323 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 19053 Z= 0.143 Angle : 0.483 14.176 25924 Z= 0.244 Chirality : 0.039 0.149 2885 Planarity : 0.004 0.044 3163 Dihedral : 7.677 121.144 2906 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: 0.10 (0.18), residues: 2178 helix: 1.25 (0.17), residues: 941 sheet: -0.17 (0.33), residues: 246 loop : -1.03 (0.19), residues: 991 =============================================================================== Job complete usr+sys time: 4288.84 seconds wall clock time: 78 minutes 29.77 seconds (4709.77 seconds total)