Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 23:45:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhn_29096/04_2023/8fhn_29096_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhn_29096/04_2023/8fhn_29096.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhn_29096/04_2023/8fhn_29096_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhn_29096/04_2023/8fhn_29096_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhn_29096/04_2023/8fhn_29096_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhn_29096/04_2023/8fhn_29096.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhn_29096/04_2023/8fhn_29096.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhn_29096/04_2023/8fhn_29096_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhn_29096/04_2023/8fhn_29096_updated.pdb" } resolution = 3.0 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= -0.001 sd= 0.051 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: 7 Type Number sf(0) Gaussians P 6 5.49 5 S 80 5.16 5 Cl 2 4.86 5 C 8847 2.51 5 N 2273 2.21 5 O 2399 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 417": "OE1" <-> "OE2" Residue "A TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 524": "OE1" <-> "OE2" Residue "A TYR 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 778": "OE1" <-> "OE2" Residue "A PHE 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 898": "OD1" <-> "OD2" Residue "A TYR 990": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 248": "OE1" <-> "OE2" Residue "B ASP 259": "OD1" <-> "OD2" Residue "B GLU 310": "OE1" <-> "OE2" Residue "B GLU 485": "OE1" <-> "OE2" Residue "B GLU 524": "OE1" <-> "OE2" Residue "B TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 755": "OE1" <-> "OE2" Residue "B PHE 822": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 966": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 167": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 13613 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 846, 6621 Classifications: {'peptide': 846} Link IDs: {'PTRANS': 37, 'TRANS': 808} Chain breaks: 2 Chain: "B" Number of atoms: 6643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 847, 6643 Classifications: {'peptide': 847} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 36, 'TRANS': 810} Chain breaks: 2 Chain: "C" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 237 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 26} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'ATP': 1, 'XZF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'ATP': 1, 'XZF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.30, per 1000 atoms: 0.54 Number of scatterers: 13613 At special positions: 0 Unit cell: (112.66, 141.9, 113.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 2 17.00 S 80 16.00 P 6 15.00 F 6 9.00 O 2399 8.00 N 2273 7.00 C 8847 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 421 " distance=2.05 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 436 " distance=2.03 Simple disulfide: pdb=" SG CYS B 416 " - pdb=" SG CYS B 421 " distance=2.04 Simple disulfide: pdb=" SG CYS B 430 " - pdb=" SG CYS B 436 " distance=2.02 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: 5.35 Conformation dependent library (CDL) restraints added in 2.0 seconds 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3172 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 74 helices and 3 sheets defined 53.9% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'A' and resid 143 through 150 Processing helix chain 'A' and resid 154 through 157 No H-bonds generated for 'chain 'A' and resid 154 through 157' Processing helix chain 'A' and resid 159 through 194 removed outlier: 6.925A pdb=" N ILE A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 9.195A pdb=" N VAL A 169 " --> pdb=" O GLN A 165 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N VAL A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR A 182 " --> pdb=" O SER A 178 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER A 193 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 211 removed outlier: 3.599A pdb=" N SER A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 No H-bonds generated for 'chain 'A' and resid 213 through 216' Processing helix chain 'A' and resid 220 through 249 removed outlier: 3.982A pdb=" N ALA A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY A 237 " --> pdb=" O MET A 233 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU A 248 " --> pdb=" O ASP A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 276 removed outlier: 3.689A pdb=" N ILE A 262 " --> pdb=" O ASN A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 305 removed outlier: 3.772A pdb=" N SER A 283 " --> pdb=" O MET A 279 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS A 284 " --> pdb=" O GLU A 280 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL A 287 " --> pdb=" O SER A 283 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 288 " --> pdb=" O LYS A 284 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 315 removed outlier: 4.242A pdb=" N LYS A 315 " --> pdb=" O ASP A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 327 Processing helix chain 'A' and resid 340 through 350 removed outlier: 3.823A pdb=" N ILE A 346 " --> pdb=" O GLY A 342 " (cutoff:3.500A) Proline residue: A 349 - end of helix Processing helix chain 'A' and resid 358 through 360 No H-bonds generated for 'chain 'A' and resid 358 through 360' Processing helix chain 'A' and resid 367 through 395 removed outlier: 3.630A pdb=" N ILE A 371 " --> pdb=" O PRO A 367 " (cutoff:3.500A) Proline residue: A 372 - end of helix removed outlier: 3.594A pdb=" N ALA A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 423 Processing helix chain 'A' and resid 428 through 433 Processing helix chain 'A' and resid 446 through 450 Processing helix chain 'A' and resid 454 through 485 removed outlier: 3.859A pdb=" N SER A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 469 " --> pdb=" O THR A 465 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER A 475 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA A 477 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N CYS A 482 " --> pdb=" O LYS A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 495 Processing helix chain 'A' and resid 508 through 522 removed outlier: 3.718A pdb=" N ILE A 522 " --> pdb=" O ALA A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 535 Processing helix chain 'A' and resid 537 through 553 removed outlier: 3.742A pdb=" N CYS A 547 " --> pdb=" O ILE A 543 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A 553 " --> pdb=" O HIS A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 584 removed outlier: 3.755A pdb=" N VAL A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N MET A 581 " --> pdb=" O SER A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 606 removed outlier: 3.730A pdb=" N LEU A 590 " --> pdb=" O TRP A 586 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE A 591 " --> pdb=" O TRP A 587 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 599 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 633 removed outlier: 3.645A pdb=" N SER A 620 " --> pdb=" O VAL A 616 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N TYR A 621 " --> pdb=" O GLN A 617 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN A 622 " --> pdb=" O ALA A 618 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR A 627 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ASN A 632 " --> pdb=" O SER A 628 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLU A 633 " --> pdb=" O VAL A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 665 removed outlier: 3.802A pdb=" N PHE A 661 " --> pdb=" O ALA A 657 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL A 662 " --> pdb=" O LEU A 658 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N PHE A 665 " --> pdb=" O PHE A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 702 Processing helix chain 'A' and resid 718 through 727 removed outlier: 3.613A pdb=" N GLN A 722 " --> pdb=" O ARG A 718 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE A 723 " --> pdb=" O ARG A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 766 removed outlier: 3.638A pdb=" N LEU A 761 " --> pdb=" O TYR A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 823 No H-bonds generated for 'chain 'A' and resid 821 through 823' Processing helix chain 'A' and resid 842 through 851 Proline residue: A 847 - end of helix Processing helix chain 'A' and resid 854 through 856 No H-bonds generated for 'chain 'A' and resid 854 through 856' Processing helix chain 'A' and resid 879 through 886 removed outlier: 3.714A pdb=" N LYS A 885 " --> pdb=" O SER A 881 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N PHE A 886 " --> pdb=" O LEU A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 914 Processing helix chain 'A' and resid 916 through 918 No H-bonds generated for 'chain 'A' and resid 916 through 918' Processing helix chain 'A' and resid 927 through 934 Processing helix chain 'A' and resid 943 through 948 Processing helix chain 'A' and resid 951 through 966 removed outlier: 3.741A pdb=" N VAL A 957 " --> pdb=" O SER A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 998 removed outlier: 4.129A pdb=" N SER A 998 " --> pdb=" O LEU A 994 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 150 removed outlier: 3.807A pdb=" N ASN B 149 " --> pdb=" O ARG B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 157 No H-bonds generated for 'chain 'B' and resid 154 through 157' Processing helix chain 'B' and resid 159 through 193 removed outlier: 6.867A pdb=" N ILE B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N VAL B 169 " --> pdb=" O GLN B 165 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU B 170 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N VAL B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N THR B 182 " --> pdb=" O SER B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 211 Processing helix chain 'B' and resid 213 through 249 removed outlier: 3.606A pdb=" N GLY B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU B 248 " --> pdb=" O ASP B 244 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 276 removed outlier: 3.570A pdb=" N VAL B 265 " --> pdb=" O ARG B 261 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL B 266 " --> pdb=" O ILE B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 303 removed outlier: 3.800A pdb=" N LYS B 284 " --> pdb=" O GLU B 280 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA B 285 " --> pdb=" O TRP B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 315 removed outlier: 3.787A pdb=" N LYS B 315 " --> pdb=" O ASP B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 325 No H-bonds generated for 'chain 'B' and resid 322 through 325' Processing helix chain 'B' and resid 340 through 350 Proline residue: B 349 - end of helix Processing helix chain 'B' and resid 358 through 363 removed outlier: 4.026A pdb=" N SER B 361 " --> pdb=" O ALA B 358 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N GLY B 362 " --> pdb=" O ASN B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 394 Proline residue: B 372 - end of helix removed outlier: 3.620A pdb=" N MET B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE B 380 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 422 No H-bonds generated for 'chain 'B' and resid 420 through 422' Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 446 through 449 No H-bonds generated for 'chain 'B' and resid 446 through 449' Processing helix chain 'B' and resid 454 through 485 removed outlier: 3.548A pdb=" N LEU B 466 " --> pdb=" O GLY B 463 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER B 467 " --> pdb=" O ALA B 464 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA B 469 " --> pdb=" O LEU B 466 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N CYS B 472 " --> pdb=" O ALA B 469 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA B 476 " --> pdb=" O LEU B 473 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS B 478 " --> pdb=" O SER B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 522 removed outlier: 3.778A pdb=" N ILE B 522 " --> pdb=" O ALA B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 532 No H-bonds generated for 'chain 'B' and resid 529 through 532' Processing helix chain 'B' and resid 535 through 552 removed outlier: 3.802A pdb=" N SER B 539 " --> pdb=" O PHE B 535 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS B 547 " --> pdb=" O ILE B 543 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE B 548 " --> pdb=" O ASN B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 584 removed outlier: 3.537A pdb=" N ALA B 574 " --> pdb=" O ALA B 570 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER B 577 " --> pdb=" O GLY B 573 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 578 " --> pdb=" O ALA B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 604 removed outlier: 3.501A pdb=" N VAL B 596 " --> pdb=" O ALA B 592 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 599 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL B 603 " --> pdb=" O LEU B 599 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE B 604 " --> pdb=" O LEU B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 632 removed outlier: 3.541A pdb=" N GLY B 630 " --> pdb=" O SER B 626 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASN B 632 " --> pdb=" O SER B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 640 No H-bonds generated for 'chain 'B' and resid 638 through 640' Processing helix chain 'B' and resid 656 through 665 removed outlier: 3.965A pdb=" N PHE B 665 " --> pdb=" O PHE B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 702 removed outlier: 3.800A pdb=" N THR B 697 " --> pdb=" O ALA B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 727 Processing helix chain 'B' and resid 751 through 766 removed outlier: 3.678A pdb=" N LEU B 761 " --> pdb=" O TYR B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 823 No H-bonds generated for 'chain 'B' and resid 821 through 823' Processing helix chain 'B' and resid 846 through 852 Processing helix chain 'B' and resid 869 through 885 removed outlier: 3.673A pdb=" N MET B 872 " --> pdb=" O ILE B 869 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ASP B 873 " --> pdb=" O ASN B 870 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN B 874 " --> pdb=" O ARG B 871 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS B 877 " --> pdb=" O GLN B 874 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 883 " --> pdb=" O ILE B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 905 through 914 Processing helix chain 'B' and resid 927 through 934 removed outlier: 3.931A pdb=" N ASN B 931 " --> pdb=" O GLU B 927 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLU B 932 " --> pdb=" O ALA B 928 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET B 933 " --> pdb=" O THR B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 947 Processing helix chain 'B' and resid 950 through 966 removed outlier: 3.547A pdb=" N GLN B 956 " --> pdb=" O LYS B 952 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL B 957 " --> pdb=" O SER B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 996 Processing helix chain 'C' and resid 165 through 169 Processing sheet with id= A, first strand: chain 'A' and resid 672 through 675 removed outlier: 6.802A pdb=" N CYS A 645 " --> pdb=" O ILE A 673 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLY A 675 " --> pdb=" O CYS A 645 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL A 647 " --> pdb=" O GLY A 675 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE A 737 " --> pdb=" O LEU A 646 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N LEU A 648 " --> pdb=" O ILE A 737 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N VAL A 739 " --> pdb=" O LEU A 648 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N GLY A 770 " --> pdb=" O LEU A 738 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL A 740 " --> pdb=" O GLY A 770 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N CYS A 772 " --> pdb=" O VAL A 740 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE A 973 " --> pdb=" O ILE A1006 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ILE A1008 " --> pdb=" O ILE A 973 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE A 975 " --> pdb=" O ILE A1008 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU A 972 " --> pdb=" O THR A 830 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR A 976 " --> pdb=" O TYR A 834 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LYS A 860 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ILE A 833 " --> pdb=" O LYS A 860 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ARG A 862 " --> pdb=" O ILE A 833 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 677 through 679 removed outlier: 6.846A pdb=" N VAL A 712 " --> pdb=" O LEU A 678 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 892 through 896 removed outlier: 3.539A pdb=" N VAL B 863 " --> pdb=" O GLU B 892 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU B 972 " --> pdb=" O ASP B 832 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N TYR B 834 " --> pdb=" O LEU B 972 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL B 974 " --> pdb=" O TYR B 834 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ILE B 975 " --> pdb=" O PRO B1004 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE B1006 " --> pdb=" O ILE B 975 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N GLY B 741 " --> pdb=" O LEU B 648 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N PHE B 708 " --> pdb=" O CYS B 674 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N HIS B 676 " --> pdb=" O PHE B 708 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N SER B 710 " --> pdb=" O HIS B 676 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LEU B 678 " --> pdb=" O SER B 710 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL B 712 " --> pdb=" O LEU B 678 " (cutoff:3.500A) 558 hydrogen bonds defined for protein. 1560 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.98 Time building geometry restraints manager: 5.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2261 1.32 - 1.45: 3756 1.45 - 1.57: 7794 1.57 - 1.69: 16 1.69 - 1.82: 121 Bond restraints: 13948 Sorted by residual: bond pdb=" C4 ATP B1101 " pdb=" C5 ATP B1101 " ideal model delta sigma weight residual 1.388 1.456 -0.068 1.00e-02 1.00e+04 4.68e+01 bond pdb=" C4 ATP A1101 " pdb=" C5 ATP A1101 " ideal model delta sigma weight residual 1.388 1.453 -0.065 1.00e-02 1.00e+04 4.28e+01 bond pdb=" C5 ATP A1101 " pdb=" C6 ATP A1101 " ideal model delta sigma weight residual 1.409 1.470 -0.061 1.00e-02 1.00e+04 3.70e+01 bond pdb=" C5 ATP B1101 " pdb=" C6 ATP B1101 " ideal model delta sigma weight residual 1.409 1.467 -0.058 1.00e-02 1.00e+04 3.33e+01 bond pdb=" C5 ATP A1101 " pdb=" N7 ATP A1101 " ideal model delta sigma weight residual 1.387 1.338 0.049 1.00e-02 1.00e+04 2.43e+01 ... (remaining 13943 not shown) Histogram of bond angle deviations from ideal: 97.15 - 105.03: 270 105.03 - 112.91: 7504 112.91 - 120.78: 6868 120.78 - 128.66: 4200 128.66 - 136.54: 132 Bond angle restraints: 18974 Sorted by residual: angle pdb=" PB ATP B1101 " pdb=" O3B ATP B1101 " pdb=" PG ATP B1101 " ideal model delta sigma weight residual 139.87 118.04 21.83 1.00e+00 1.00e+00 4.77e+02 angle pdb=" PB ATP A1101 " pdb=" O3B ATP A1101 " pdb=" PG ATP A1101 " ideal model delta sigma weight residual 139.87 118.43 21.44 1.00e+00 1.00e+00 4.60e+02 angle pdb=" PA ATP A1101 " pdb=" O3A ATP A1101 " pdb=" PB ATP A1101 " ideal model delta sigma weight residual 136.83 116.66 20.17 1.00e+00 1.00e+00 4.07e+02 angle pdb=" PA ATP B1101 " pdb=" O3A ATP B1101 " pdb=" PB ATP B1101 " ideal model delta sigma weight residual 136.83 117.78 19.05 1.00e+00 1.00e+00 3.63e+02 angle pdb=" N SER A 319 " pdb=" CA SER A 319 " pdb=" C SER A 319 " ideal model delta sigma weight residual 111.07 121.59 -10.52 1.07e+00 8.73e-01 9.67e+01 ... (remaining 18969 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 7296 17.19 - 34.38: 654 34.38 - 51.57: 139 51.57 - 68.77: 43 68.77 - 85.96: 14 Dihedral angle restraints: 8146 sinusoidal: 3200 harmonic: 4946 Sorted by residual: dihedral pdb=" CB CYS B 416 " pdb=" SG CYS B 416 " pdb=" SG CYS B 421 " pdb=" CB CYS B 421 " ideal model delta sinusoidal sigma weight residual 93.00 11.59 81.41 1 1.00e+01 1.00e-02 8.17e+01 dihedral pdb=" CA ASN A 258 " pdb=" C ASN A 258 " pdb=" N ASP A 259 " pdb=" CA ASP A 259 " ideal model delta harmonic sigma weight residual 180.00 153.26 26.74 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA CYS A 436 " pdb=" C CYS A 436 " pdb=" N HIS A 437 " pdb=" CA HIS A 437 " ideal model delta harmonic sigma weight residual -180.00 -154.45 -25.55 0 5.00e+00 4.00e-02 2.61e+01 ... (remaining 8143 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1933 0.084 - 0.169: 189 0.169 - 0.253: 20 0.253 - 0.337: 9 0.337 - 0.421: 1 Chirality restraints: 2152 Sorted by residual: chirality pdb=" CA ARG B 685 " pdb=" N ARG B 685 " pdb=" C ARG B 685 " pdb=" CB ARG B 685 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.44e+00 chirality pdb=" CA TYR B 499 " pdb=" N TYR B 499 " pdb=" C TYR B 499 " pdb=" CB TYR B 499 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CA PHE B 494 " pdb=" N PHE B 494 " pdb=" C PHE B 494 " pdb=" CB PHE B 494 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.54e+00 ... (remaining 2149 not shown) Planarity restraints: 2353 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 678 " 0.014 2.00e-02 2.50e+03 2.92e-02 8.51e+00 pdb=" C LEU B 678 " -0.050 2.00e-02 2.50e+03 pdb=" O LEU B 678 " 0.019 2.00e-02 2.50e+03 pdb=" N ILE B 679 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 255 " -0.040 5.00e-02 4.00e+02 6.23e-02 6.21e+00 pdb=" N PRO A 256 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 256 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 256 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 902 " 0.038 5.00e-02 4.00e+02 5.92e-02 5.60e+00 pdb=" N PRO A 903 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 903 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 903 " 0.035 5.00e-02 4.00e+02 ... (remaining 2350 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1546 2.74 - 3.28: 13159 3.28 - 3.82: 21443 3.82 - 4.36: 26228 4.36 - 4.90: 45767 Nonbonded interactions: 108143 Sorted by model distance: nonbonded pdb=" O HIS B 750 " pdb=" OG1 THR B 753 " model vdw 2.199 2.440 nonbonded pdb=" NH2 ARG B 703 " pdb=" O ALA B 818 " model vdw 2.220 2.520 nonbonded pdb=" OH TYR B 156 " pdb=" OG SER B 296 " model vdw 2.229 2.440 nonbonded pdb=" O PRO B 530 " pdb=" ND2 ASN B 534 " model vdw 2.230 2.520 nonbonded pdb=" OD2 ASP B 839 " pdb=" OG1 THR B 843 " model vdw 2.230 2.440 ... (remaining 108138 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 131 through 605 or resid 620 through 1018 or resid 1101 th \ rough 1102)) selection = (chain 'B' and (resid 131 through 865 or resid 878 through 1018 or resid 1101 th \ rough 1102)) } 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: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.960 Check model and map are aligned: 0.200 Set scattering table: 0.110 Process input model: 36.220 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 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 0.068 13948 Z= 0.565 Angle : 0.988 21.835 18974 Z= 0.628 Chirality : 0.058 0.421 2152 Planarity : 0.006 0.062 2353 Dihedral : 14.565 85.958 4962 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer Outliers : 2.21 % Cbeta Deviations : 0.06 % 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: -1.79 (0.19), residues: 1706 helix: -0.63 (0.17), residues: 918 sheet: -0.65 (0.50), residues: 111 loop : -1.97 (0.21), residues: 677 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 179 time to evaluate : 1.842 Fit side-chains outliers start: 32 outliers final: 4 residues processed: 204 average time/residue: 1.3803 time to fit residues: 306.2199 Evaluate side-chains 138 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 134 time to evaluate : 1.586 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 2.1885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 133 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 154 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 HIS A 258 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 GLN A 956 GLN A1014 ASN B 149 ASN B 359 ASN B 406 ASN B 481 GLN B 502 ASN B 644 GLN B 696 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 13948 Z= 0.188 Angle : 0.552 7.636 18974 Z= 0.286 Chirality : 0.041 0.185 2152 Planarity : 0.004 0.040 2353 Dihedral : 5.969 84.330 1873 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer Outliers : 2.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.20), residues: 1706 helix: 0.20 (0.17), residues: 921 sheet: -0.64 (0.47), residues: 124 loop : -1.79 (0.22), residues: 661 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 152 time to evaluate : 1.544 Fit side-chains outliers start: 30 outliers final: 10 residues processed: 173 average time/residue: 1.2479 time to fit residues: 237.7338 Evaluate side-chains 142 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 132 time to evaluate : 1.466 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 3 average time/residue: 0.1382 time to fit residues: 2.6997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 153 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 GLN A 900 ASN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 ASN B 781 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 13948 Z= 0.195 Angle : 0.520 7.150 18974 Z= 0.264 Chirality : 0.041 0.143 2152 Planarity : 0.004 0.038 2353 Dihedral : 5.644 86.675 1873 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer Outliers : 2.48 % 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: -0.53 (0.20), residues: 1706 helix: 0.57 (0.18), residues: 923 sheet: -0.39 (0.46), residues: 125 loop : -1.63 (0.22), residues: 658 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 142 time to evaluate : 1.703 Fit side-chains outliers start: 36 outliers final: 16 residues processed: 164 average time/residue: 1.1747 time to fit residues: 213.8652 Evaluate side-chains 146 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 130 time to evaluate : 1.528 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 11 residues processed: 5 average time/residue: 0.3363 time to fit residues: 4.2750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 chunk 155 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 81 optimal weight: 0.0980 chunk 147 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1014 ASN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 13948 Z= 0.196 Angle : 0.503 6.897 18974 Z= 0.256 Chirality : 0.041 0.156 2152 Planarity : 0.004 0.038 2353 Dihedral : 5.477 87.528 1873 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer Outliers : 2.41 % 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: -0.32 (0.20), residues: 1706 helix: 0.75 (0.18), residues: 923 sheet: -0.21 (0.46), residues: 125 loop : -1.58 (0.22), residues: 658 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 142 time to evaluate : 1.552 Fit side-chains outliers start: 35 outliers final: 19 residues processed: 166 average time/residue: 1.2488 time to fit residues: 228.6194 Evaluate side-chains 153 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 134 time to evaluate : 1.610 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 15 residues processed: 4 average time/residue: 0.1528 time to fit residues: 3.3533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 13948 Z= 0.274 Angle : 0.542 7.717 18974 Z= 0.274 Chirality : 0.042 0.177 2152 Planarity : 0.004 0.040 2353 Dihedral : 5.531 87.330 1873 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer Outliers : 3.03 % 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: -0.39 (0.20), residues: 1706 helix: 0.67 (0.18), residues: 926 sheet: -0.16 (0.46), residues: 125 loop : -1.59 (0.22), residues: 655 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 136 time to evaluate : 1.850 Fit side-chains revert: symmetry clash outliers start: 44 outliers final: 25 residues processed: 170 average time/residue: 1.2057 time to fit residues: 226.8385 Evaluate side-chains 157 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 132 time to evaluate : 1.462 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 18 residues processed: 8 average time/residue: 0.2785 time to fit residues: 5.1462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 0.7980 chunk 147 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 96 optimal weight: 7.9990 chunk 40 optimal weight: 0.6980 chunk 164 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1014 ASN B 502 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 13948 Z= 0.198 Angle : 0.507 7.711 18974 Z= 0.256 Chirality : 0.041 0.179 2152 Planarity : 0.004 0.039 2353 Dihedral : 5.367 88.407 1873 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer Outliers : 2.62 % 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: -0.22 (0.20), residues: 1706 helix: 0.79 (0.18), residues: 929 sheet: -0.02 (0.46), residues: 125 loop : -1.53 (0.22), residues: 652 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 136 time to evaluate : 1.655 Fit side-chains revert: symmetry clash outliers start: 38 outliers final: 25 residues processed: 165 average time/residue: 1.1931 time to fit residues: 217.9003 Evaluate side-chains 155 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 130 time to evaluate : 1.541 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 20 residues processed: 5 average time/residue: 0.1535 time to fit residues: 3.4881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 3.9990 chunk 18 optimal weight: 0.0010 chunk 93 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 overall best weight: 1.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 ASN B 502 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 13948 Z= 0.191 Angle : 0.501 7.102 18974 Z= 0.254 Chirality : 0.040 0.158 2152 Planarity : 0.004 0.039 2353 Dihedral : 5.270 88.473 1873 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.58 % Favored : 97.36 % Rotamer Outliers : 2.62 % 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: -0.15 (0.20), residues: 1706 helix: 0.83 (0.18), residues: 933 sheet: 0.00 (0.45), residues: 131 loop : -1.50 (0.23), residues: 642 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 135 time to evaluate : 1.468 Fit side-chains revert: symmetry clash outliers start: 38 outliers final: 21 residues processed: 166 average time/residue: 1.2102 time to fit residues: 221.9153 Evaluate side-chains 150 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 129 time to evaluate : 1.597 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 18 residues processed: 3 average time/residue: 0.1662 time to fit residues: 3.1228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 81 optimal weight: 0.1980 chunk 15 optimal weight: 0.0870 chunk 128 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.6562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1014 ASN B 406 ASN B 502 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 13948 Z= 0.148 Angle : 0.480 7.768 18974 Z= 0.243 Chirality : 0.040 0.164 2152 Planarity : 0.003 0.039 2353 Dihedral : 5.115 89.361 1873 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.34 % Favored : 97.60 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.21), residues: 1706 helix: 0.99 (0.18), residues: 931 sheet: 0.09 (0.44), residues: 134 loop : -1.46 (0.23), residues: 641 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 138 time to evaluate : 1.551 Fit side-chains outliers start: 26 outliers final: 20 residues processed: 162 average time/residue: 1.2593 time to fit residues: 225.6370 Evaluate side-chains 153 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 133 time to evaluate : 1.566 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 19 residues processed: 1 average time/residue: 1.1885 time to fit residues: 3.5075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 4.9990 chunk 143 optimal weight: 0.9990 chunk 152 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 66 optimal weight: 0.4980 chunk 119 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 161 optimal weight: 0.2980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 ASN B 502 ASN B 931 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 13948 Z= 0.168 Angle : 0.489 7.208 18974 Z= 0.247 Chirality : 0.040 0.144 2152 Planarity : 0.003 0.039 2353 Dihedral : 5.063 89.158 1873 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.46 % Favored : 97.48 % Rotamer Outliers : 1.86 % 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: 0.11 (0.21), residues: 1706 helix: 1.05 (0.18), residues: 929 sheet: 0.18 (0.44), residues: 134 loop : -1.41 (0.23), residues: 643 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 135 time to evaluate : 1.713 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 21 residues processed: 159 average time/residue: 1.2004 time to fit residues: 211.9634 Evaluate side-chains 153 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 132 time to evaluate : 1.526 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 19 residues processed: 2 average time/residue: 0.2299 time to fit residues: 2.8505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 6.9990 chunk 76 optimal weight: 0.4980 chunk 112 optimal weight: 0.5980 chunk 169 optimal weight: 5.9990 chunk 155 optimal weight: 0.7980 chunk 134 optimal weight: 0.6980 chunk 14 optimal weight: 6.9990 chunk 104 optimal weight: 0.4980 chunk 82 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1014 ASN B 406 ASN B 502 ASN B 931 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 13948 Z= 0.143 Angle : 0.476 11.165 18974 Z= 0.240 Chirality : 0.039 0.140 2152 Planarity : 0.003 0.039 2353 Dihedral : 4.945 89.492 1873 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.40 % Favored : 97.54 % Rotamer Outliers : 1.38 % 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: 0.23 (0.21), residues: 1706 helix: 1.12 (0.18), residues: 931 sheet: 0.34 (0.44), residues: 134 loop : -1.33 (0.23), residues: 641 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 138 time to evaluate : 1.922 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 19 residues processed: 158 average time/residue: 1.2676 time to fit residues: 221.2366 Evaluate side-chains 149 residues out of total 1452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 130 time to evaluate : 1.653 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 19 residues processed: 0 time to fit residues: 2.3548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 37 optimal weight: 0.4980 chunk 135 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 ASN B 502 ASN B 931 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.169026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.123508 restraints weight = 15968.527| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.30 r_work: 0.3447 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 13948 Z= 0.163 Angle : 0.485 9.637 18974 Z= 0.243 Chirality : 0.040 0.140 2152 Planarity : 0.003 0.039 2353 Dihedral : 4.928 89.070 1873 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.52 % Favored : 97.42 % Rotamer Outliers : 2.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.21), residues: 1706 helix: 1.19 (0.18), residues: 929 sheet: 0.41 (0.44), residues: 134 loop : -1.34 (0.23), residues: 643 =============================================================================== Job complete usr+sys time: 4525.92 seconds wall clock time: 81 minutes 29.75 seconds (4889.75 seconds total)