Starting phenix.real_space_refine on Mon Apr 8 01:56:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzd_41755/04_2024/8tzd_41755_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzd_41755/04_2024/8tzd_41755.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzd_41755/04_2024/8tzd_41755_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzd_41755/04_2024/8tzd_41755_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzd_41755/04_2024/8tzd_41755_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzd_41755/04_2024/8tzd_41755.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzd_41755/04_2024/8tzd_41755.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzd_41755/04_2024/8tzd_41755_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzd_41755/04_2024/8tzd_41755_neut_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.062 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 85 5.16 5 C 8073 2.51 5 N 1908 2.21 5 O 2108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 12175 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3971 Classifications: {'peptide': 521} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 18, 'TRANS': 502} Chain breaks: 1 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 73 Chain: "B" Number of atoms: 4053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4053 Classifications: {'peptide': 533} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 77 Chain: "C" Number of atoms: 4053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4053 Classifications: {'peptide': 533} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 77 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {'LBN': 1, 'XMO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'XMO': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'XMO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.69, per 1000 atoms: 0.55 Number of scatterers: 12175 At special positions: 0 Unit cell: (129.6, 127.44, 79.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 85 16.00 P 1 15.00 O 2108 8.00 N 1908 7.00 C 8073 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=0, symmetry=0 Time building additional restraints: 5.45 Conformation dependent library (CDL) restraints added in 2.2 seconds 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2924 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 76 helices and 0 sheets defined 81.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.50 Creating SS restraints... Processing helix chain 'A' and resid 91 through 102 Processing helix chain 'A' and resid 104 through 129 Processing helix chain 'A' and resid 135 through 156 Processing helix chain 'A' and resid 158 through 197 Proline residue: A 167 - end of helix removed outlier: 5.021A pdb=" N PHE A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N TRP A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N TRP A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 182 " --> pdb=" O TRP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 202 No H-bonds generated for 'chain 'A' and resid 199 through 202' Processing helix chain 'A' and resid 204 through 222 removed outlier: 3.570A pdb=" N VAL A 208 " --> pdb=" O GLN A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 250 Processing helix chain 'A' and resid 253 through 280 removed outlier: 3.628A pdb=" N PHE A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N TYR A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER A 273 " --> pdb=" O PHE A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 287 No H-bonds generated for 'chain 'A' and resid 285 through 287' Processing helix chain 'A' and resid 289 through 311 removed outlier: 4.539A pdb=" N LEU A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Proline residue: A 296 - end of helix Processing helix chain 'A' and resid 313 through 328 Processing helix chain 'A' and resid 333 through 343 removed outlier: 3.668A pdb=" N ILE A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 360 Proline residue: A 351 - end of helix removed outlier: 4.345A pdb=" N VAL A 354 " --> pdb=" O SER A 350 " (cutoff:3.500A) Proline residue: A 356 - end of helix Proline residue: A 359 - end of helix Processing helix chain 'A' and resid 363 through 374 Processing helix chain 'A' and resid 379 through 388 Processing helix chain 'A' and resid 392 through 413 removed outlier: 4.180A pdb=" N ALA A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 438 through 481 removed outlier: 3.963A pdb=" N ALA A 454 " --> pdb=" O ILE A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 495 Processing helix chain 'A' and resid 497 through 503 Processing helix chain 'A' and resid 508 through 522 removed outlier: 4.188A pdb=" N PHE A 511 " --> pdb=" O GLN A 508 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET A 512 " --> pdb=" O ASP A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 541 Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 587 through 593 removed outlier: 4.792A pdb=" N ARG A 591 " --> pdb=" O SER A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 618 Processing helix chain 'B' and resid 91 through 102 Processing helix chain 'B' and resid 104 through 129 Processing helix chain 'B' and resid 135 through 156 Processing helix chain 'B' and resid 158 through 202 Proline residue: B 167 - end of helix removed outlier: 4.678A pdb=" N PHE B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N TRP B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N TRP B 181 " --> pdb=" O PHE B 177 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 222 Processing helix chain 'B' and resid 232 through 249 Processing helix chain 'B' and resid 253 through 281 removed outlier: 4.089A pdb=" N TYR B 272 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N SER B 273 " --> pdb=" O PHE B 269 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ASP B 274 " --> pdb=" O LEU B 270 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ALA B 275 " --> pdb=" O GLY B 271 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLY B 276 " --> pdb=" O TYR B 272 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE B 279 " --> pdb=" O ALA B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 287 No H-bonds generated for 'chain 'B' and resid 285 through 287' Processing helix chain 'B' and resid 289 through 311 removed outlier: 4.292A pdb=" N LEU B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Proline residue: B 296 - end of helix Processing helix chain 'B' and resid 313 through 329 removed outlier: 3.622A pdb=" N ILE B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 343 removed outlier: 3.825A pdb=" N ILE B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 360 Proline residue: B 351 - end of helix removed outlier: 4.809A pdb=" N VAL B 354 " --> pdb=" O SER B 350 " (cutoff:3.500A) Proline residue: B 356 - end of helix Proline residue: B 359 - end of helix Processing helix chain 'B' and resid 363 through 375 Processing helix chain 'B' and resid 379 through 387 removed outlier: 4.017A pdb=" N GLY B 383 " --> pdb=" O GLY B 379 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA B 384 " --> pdb=" O SER B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 413 Proline residue: B 404 - end of helix Processing helix chain 'B' and resid 424 through 428 Processing helix chain 'B' and resid 438 through 481 removed outlier: 3.665A pdb=" N ILE B 450 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER B 451 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N MET B 480 " --> pdb=" O TRP B 476 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N PHE B 481 " --> pdb=" O LEU B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 495 removed outlier: 3.598A pdb=" N TYR B 494 " --> pdb=" O VAL B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 503 Processing helix chain 'B' and resid 508 through 522 removed outlier: 4.045A pdb=" N PHE B 511 " --> pdb=" O GLN B 508 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL B 513 " --> pdb=" O SER B 510 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE B 522 " --> pdb=" O TYR B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 541 Processing helix chain 'B' and resid 556 through 565 Processing helix chain 'B' and resid 573 through 585 removed outlier: 4.700A pdb=" N ILE B 577 " --> pdb=" O GLY B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 595 removed outlier: 4.979A pdb=" N ARG B 591 " --> pdb=" O SER B 588 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR B 594 " --> pdb=" O ARG B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 618 removed outlier: 3.621A pdb=" N LEU B 601 " --> pdb=" O ALA B 597 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 602 " --> pdb=" O MET B 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 102 Processing helix chain 'C' and resid 104 through 129 Processing helix chain 'C' and resid 131 through 156 Proline residue: C 136 - end of helix Processing helix chain 'C' and resid 158 through 202 Proline residue: C 167 - end of helix removed outlier: 4.405A pdb=" N PHE C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N TRP C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N TRP C 181 " --> pdb=" O PHE C 177 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL C 182 " --> pdb=" O TRP C 178 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA C 200 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LYS C 201 " --> pdb=" O PHE C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 222 Processing helix chain 'C' and resid 233 through 250 Processing helix chain 'C' and resid 253 through 276 removed outlier: 4.015A pdb=" N SER C 273 " --> pdb=" O PHE C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 281 No H-bonds generated for 'chain 'C' and resid 278 through 281' Processing helix chain 'C' and resid 285 through 287 No H-bonds generated for 'chain 'C' and resid 285 through 287' Processing helix chain 'C' and resid 289 through 311 removed outlier: 4.322A pdb=" N LEU C 295 " --> pdb=" O ALA C 291 " (cutoff:3.500A) Proline residue: C 296 - end of helix Processing helix chain 'C' and resid 313 through 328 removed outlier: 3.587A pdb=" N THR C 328 " --> pdb=" O VAL C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 340 Processing helix chain 'C' and resid 347 through 360 Proline residue: C 351 - end of helix removed outlier: 4.689A pdb=" N VAL C 354 " --> pdb=" O SER C 350 " (cutoff:3.500A) Proline residue: C 356 - end of helix Proline residue: C 359 - end of helix Processing helix chain 'C' and resid 363 through 374 Processing helix chain 'C' and resid 380 through 388 removed outlier: 4.583A pdb=" N ALA C 384 " --> pdb=" O SER C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 413 removed outlier: 4.217A pdb=" N ALA C 403 " --> pdb=" O SER C 399 " (cutoff:3.500A) Proline residue: C 404 - end of helix Processing helix chain 'C' and resid 424 through 428 Processing helix chain 'C' and resid 438 through 481 removed outlier: 4.138A pdb=" N ILE C 450 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N SER C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU C 452 " --> pdb=" O SER C 448 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N MET C 480 " --> pdb=" O TRP C 476 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N PHE C 481 " --> pdb=" O LEU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 495 removed outlier: 4.521A pdb=" N TYR C 494 " --> pdb=" O VAL C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 502 Processing helix chain 'C' and resid 508 through 522 removed outlier: 4.200A pdb=" N PHE C 511 " --> pdb=" O GLN C 508 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET C 512 " --> pdb=" O ASP C 509 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL C 513 " --> pdb=" O SER C 510 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE C 522 " --> pdb=" O TYR C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 541 Processing helix chain 'C' and resid 556 through 565 Processing helix chain 'C' and resid 574 through 585 removed outlier: 3.810A pdb=" N ILE C 579 " --> pdb=" O LEU C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 595 removed outlier: 4.869A pdb=" N ARG C 591 " --> pdb=" O SER C 588 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR C 594 " --> pdb=" O ARG C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 618 removed outlier: 3.598A pdb=" N LEU C 618 " --> pdb=" O ILE C 614 " (cutoff:3.500A) 868 hydrogen bonds defined for protein. 2445 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: 3.64 Time building geometry restraints manager: 5.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 1821 1.29 - 1.42: 3476 1.42 - 1.55: 7045 1.55 - 1.68: 14 1.68 - 1.81: 153 Bond restraints: 12509 Sorted by residual: bond pdb=" O4 LBN A 702 " pdb=" P1 LBN A 702 " ideal model delta sigma weight residual 1.497 1.645 -0.148 2.00e-02 2.50e+03 5.47e+01 bond pdb=" O2 LBN A 702 " pdb=" P1 LBN A 702 " ideal model delta sigma weight residual 1.650 1.510 0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" C34 LBN A 702 " pdb=" O7 LBN A 702 " ideal model delta sigma weight residual 1.331 1.427 -0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" C25 LBN A 702 " pdb=" O5 LBN A 702 " ideal model delta sigma weight residual 1.326 1.406 -0.080 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C04 XMO A 701 " pdb=" O06 XMO A 701 " ideal model delta sigma weight residual 1.416 1.479 -0.063 2.00e-02 2.50e+03 1.00e+01 ... (remaining 12504 not shown) Histogram of bond angle deviations from ideal: 99.31 - 106.27: 307 106.27 - 113.23: 6847 113.23 - 120.19: 4729 120.19 - 127.15: 4990 127.15 - 134.11: 166 Bond angle restraints: 17039 Sorted by residual: angle pdb=" O1 LBN A 702 " pdb=" P1 LBN A 702 " pdb=" O2 LBN A 702 " ideal model delta sigma weight residual 93.45 109.54 -16.09 3.00e+00 1.11e-01 2.87e+01 angle pdb=" O3 LBN A 702 " pdb=" P1 LBN A 702 " pdb=" O4 LBN A 702 " ideal model delta sigma weight residual 119.36 109.58 9.78 3.00e+00 1.11e-01 1.06e+01 angle pdb=" C26 LBN A 702 " pdb=" C25 LBN A 702 " pdb=" O5 LBN A 702 " ideal model delta sigma weight residual 111.43 120.73 -9.30 3.00e+00 1.11e-01 9.62e+00 angle pdb=" C35 LBN A 702 " pdb=" C34 LBN A 702 " pdb=" O7 LBN A 702 " ideal model delta sigma weight residual 111.21 119.63 -8.42 3.00e+00 1.11e-01 7.88e+00 angle pdb=" C41 LBN A 702 " pdb=" C42 LBN A 702 " pdb=" C5 LBN A 702 " ideal model delta sigma weight residual 127.55 120.30 7.25 3.00e+00 1.11e-01 5.84e+00 ... (remaining 17034 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.29: 6910 26.29 - 52.57: 188 52.57 - 78.86: 23 78.86 - 105.14: 3 105.14 - 131.43: 3 Dihedral angle restraints: 7127 sinusoidal: 2569 harmonic: 4558 Sorted by residual: dihedral pdb=" C40 LBN A 702 " pdb=" C41 LBN A 702 " pdb=" C42 LBN A 702 " pdb=" C5 LBN A 702 " ideal model delta sinusoidal sigma weight residual 117.80 -110.77 -131.43 1 3.00e+01 1.11e-03 1.77e+01 dihedral pdb=" C01 XMO C 701 " pdb=" C02 XMO C 701 " pdb=" C04 XMO C 701 " pdb=" O06 XMO C 701 " ideal model delta sinusoidal sigma weight residual 259.35 128.22 131.13 1 3.00e+01 1.11e-03 1.77e+01 dihedral pdb=" C01 XMO B 701 " pdb=" C02 XMO B 701 " pdb=" C04 XMO B 701 " pdb=" O06 XMO B 701 " ideal model delta sinusoidal sigma weight residual 259.35 145.76 113.59 1 3.00e+01 1.11e-03 1.49e+01 ... (remaining 7124 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1384 0.033 - 0.067: 418 0.067 - 0.100: 138 0.100 - 0.133: 32 0.133 - 0.167: 2 Chirality restraints: 1974 Sorted by residual: chirality pdb=" C2 LBN A 702 " pdb=" C1 LBN A 702 " pdb=" C3 LBN A 702 " pdb=" O7 LBN A 702 " both_signs ideal model delta sigma weight residual False -2.36 -2.53 0.17 2.00e-01 2.50e+01 6.93e-01 chirality pdb=" CB ILE A 450 " pdb=" CA ILE A 450 " pdb=" CG1 ILE A 450 " pdb=" CG2 ILE A 450 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CA PRO C 234 " pdb=" N PRO C 234 " pdb=" C PRO C 234 " pdb=" CB PRO C 234 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.22e-01 ... (remaining 1971 not shown) Planarity restraints: 2069 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 233 " -0.042 5.00e-02 4.00e+02 6.40e-02 6.56e+00 pdb=" N PRO A 234 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 234 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 234 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 233 " -0.041 5.00e-02 4.00e+02 6.16e-02 6.07e+00 pdb=" N PRO C 234 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO C 234 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 234 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 403 " 0.039 5.00e-02 4.00e+02 5.87e-02 5.51e+00 pdb=" N PRO A 404 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 404 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 404 " 0.033 5.00e-02 4.00e+02 ... (remaining 2066 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 662 2.73 - 3.27: 13056 3.27 - 3.81: 20648 3.81 - 4.36: 23060 4.36 - 4.90: 41532 Nonbonded interactions: 98958 Sorted by model distance: nonbonded pdb=" OG SER B 380 " pdb=" O21 XMO B 701 " model vdw 2.183 2.440 nonbonded pdb=" O LEU B 195 " pdb=" OG1 THR B 199 " model vdw 2.203 2.440 nonbonded pdb=" O LEU A 248 " pdb=" OG1 THR A 252 " model vdw 2.227 2.440 nonbonded pdb=" O ALA A 275 " pdb=" OG SER A 278 " model vdw 2.266 2.440 nonbonded pdb=" OG SER C 574 " pdb=" O22 XMO C 701 " model vdw 2.322 2.440 ... (remaining 98953 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 90 through 622 or resid 701)) selection = (chain 'B' and (resid 90 through 421 or resid 434 through 622 or resid 701)) selection = (chain 'C' and (resid 90 through 421 or resid 434 through 622 or resid 701)) } 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: 1.090 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: 4.160 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 35.350 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 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 : 0.005 0.148 12509 Z= 0.324 Angle : 0.529 16.085 17039 Z= 0.282 Chirality : 0.036 0.167 1974 Planarity : 0.004 0.064 2069 Dihedral : 12.710 131.430 4203 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.32 % Allowed : 1.37 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.98 (0.21), residues: 1579 helix: 2.47 (0.15), residues: 1291 sheet: None (None), residues: 0 loop : -0.42 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 316 HIS 0.003 0.001 HIS A 132 PHE 0.017 0.001 PHE B 413 TYR 0.008 0.001 TYR B 231 ARG 0.002 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 220 time to evaluate : 1.295 Fit side-chains REVERT: A 284 LYS cc_start: 0.8586 (mttm) cc_final: 0.8025 (mmtt) REVERT: A 307 MET cc_start: 0.8627 (mtp) cc_final: 0.8411 (mtp) REVERT: A 470 MET cc_start: 0.8183 (mmt) cc_final: 0.7782 (mmt) REVERT: A 564 TYR cc_start: 0.8569 (m-80) cc_final: 0.8171 (m-80) REVERT: B 154 MET cc_start: 0.6859 (tpt) cc_final: 0.6308 (tpt) REVERT: B 195 LEU cc_start: 0.7310 (tt) cc_final: 0.7105 (tp) REVERT: B 305 MET cc_start: 0.7951 (mmt) cc_final: 0.7665 (mmp) REVERT: B 355 ARG cc_start: 0.8011 (tmm-80) cc_final: 0.7598 (ttm170) REVERT: B 357 TYR cc_start: 0.7682 (m-80) cc_final: 0.7481 (m-80) REVERT: C 252 THR cc_start: 0.8490 (m) cc_final: 0.8171 (p) REVERT: C 423 ASN cc_start: 0.7887 (t0) cc_final: 0.7678 (t0) REVERT: C 502 MET cc_start: 0.7559 (mmp) cc_final: 0.6769 (mtp) REVERT: C 562 SER cc_start: 0.9009 (t) cc_final: 0.8619 (m) outliers start: 4 outliers final: 3 residues processed: 224 average time/residue: 0.2228 time to fit residues: 74.2365 Evaluate side-chains 180 residues out of total 1325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 177 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 571 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 66 optimal weight: 0.0980 chunk 40 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 123 optimal weight: 0.0980 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 HIS A 444 GLN B 444 GLN ** C 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12509 Z= 0.175 Angle : 0.469 6.988 17039 Z= 0.241 Chirality : 0.037 0.144 1974 Planarity : 0.004 0.050 2069 Dihedral : 7.811 125.838 1717 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.29 % Allowed : 7.26 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.06 (0.21), residues: 1579 helix: 2.54 (0.14), residues: 1299 sheet: None (None), residues: 0 loop : -0.57 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 316 HIS 0.003 0.001 HIS C 394 PHE 0.016 0.001 PHE B 546 TYR 0.017 0.001 TYR A 385 ARG 0.003 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 179 time to evaluate : 1.366 Fit side-chains REVERT: A 154 MET cc_start: 0.6678 (tpp) cc_final: 0.6395 (tpp) REVERT: A 284 LYS cc_start: 0.8655 (mttm) cc_final: 0.8081 (mmtt) REVERT: A 307 MET cc_start: 0.8539 (mtp) cc_final: 0.8297 (mtp) REVERT: B 145 ILE cc_start: 0.7809 (mm) cc_final: 0.7591 (pt) REVERT: B 305 MET cc_start: 0.8072 (mmt) cc_final: 0.7843 (mmp) REVERT: B 314 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8359 (ptm) REVERT: B 355 ARG cc_start: 0.7994 (tmm-80) cc_final: 0.7539 (ttm170) REVERT: B 357 TYR cc_start: 0.7686 (m-80) cc_final: 0.7403 (m-80) REVERT: B 482 ASP cc_start: 0.8895 (t0) cc_final: 0.8630 (t0) REVERT: C 502 MET cc_start: 0.7352 (mmp) cc_final: 0.6623 (mtp) REVERT: C 556 MET cc_start: 0.7359 (mtt) cc_final: 0.7096 (mtp) REVERT: C 562 SER cc_start: 0.9003 (t) cc_final: 0.8607 (m) outliers start: 16 outliers final: 11 residues processed: 192 average time/residue: 0.2126 time to fit residues: 61.7182 Evaluate side-chains 179 residues out of total 1325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 167 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 584 SER Chi-restraints excluded: chain C residue 621 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 0.9990 chunk 44 optimal weight: 9.9990 chunk 119 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 142 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 267 GLN ** C 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12509 Z= 0.262 Angle : 0.498 7.587 17039 Z= 0.258 Chirality : 0.038 0.168 1974 Planarity : 0.004 0.046 2069 Dihedral : 7.386 127.949 1716 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.53 % Allowed : 9.19 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.21), residues: 1579 helix: 2.22 (0.14), residues: 1300 sheet: None (None), residues: 0 loop : -0.74 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 316 HIS 0.003 0.001 HIS A 367 PHE 0.019 0.001 PHE B 413 TYR 0.015 0.001 TYR A 564 ARG 0.002 0.000 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 173 time to evaluate : 1.319 Fit side-chains REVERT: A 152 HIS cc_start: 0.7382 (t70) cc_final: 0.7072 (t70) REVERT: A 154 MET cc_start: 0.6820 (tpp) cc_final: 0.6544 (tpp) REVERT: A 284 LYS cc_start: 0.8682 (mttm) cc_final: 0.8086 (mmtt) REVERT: B 145 ILE cc_start: 0.7784 (mm) cc_final: 0.7560 (pt) REVERT: B 160 GLN cc_start: 0.7030 (mp10) cc_final: 0.6614 (tp40) REVERT: B 314 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.8468 (ptm) REVERT: B 355 ARG cc_start: 0.8008 (tmm-80) cc_final: 0.7593 (ttm170) REVERT: B 357 TYR cc_start: 0.7728 (m-80) cc_final: 0.7391 (m-80) REVERT: C 150 TRP cc_start: 0.7841 (t-100) cc_final: 0.7639 (t-100) REVERT: C 502 MET cc_start: 0.7448 (mmp) cc_final: 0.6645 (mtp) outliers start: 19 outliers final: 15 residues processed: 186 average time/residue: 0.2204 time to fit residues: 61.0048 Evaluate side-chains 178 residues out of total 1325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 162 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 584 SER Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 621 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 144 optimal weight: 0.4980 chunk 152 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 552 GLN C 423 ASN ** C 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12509 Z= 0.169 Angle : 0.445 7.062 17039 Z= 0.228 Chirality : 0.036 0.146 1974 Planarity : 0.004 0.046 2069 Dihedral : 7.130 126.762 1716 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.69 % Allowed : 9.92 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.21), residues: 1579 helix: 2.38 (0.14), residues: 1298 sheet: None (None), residues: 0 loop : -0.76 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 316 HIS 0.002 0.000 HIS C 394 PHE 0.023 0.001 PHE A 146 TYR 0.008 0.001 TYR A 564 ARG 0.002 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 166 time to evaluate : 1.305 Fit side-chains REVERT: A 152 HIS cc_start: 0.7342 (t70) cc_final: 0.7008 (t70) REVERT: A 284 LYS cc_start: 0.8706 (mttm) cc_final: 0.8098 (mmtt) REVERT: A 564 TYR cc_start: 0.8521 (m-80) cc_final: 0.8303 (m-80) REVERT: B 248 LEU cc_start: 0.8339 (tp) cc_final: 0.7749 (mp) REVERT: B 355 ARG cc_start: 0.7968 (tmm-80) cc_final: 0.7663 (ttm170) REVERT: B 357 TYR cc_start: 0.7717 (m-80) cc_final: 0.7370 (m-80) REVERT: B 482 ASP cc_start: 0.8797 (t0) cc_final: 0.8588 (t0) REVERT: C 502 MET cc_start: 0.7396 (mmp) cc_final: 0.6591 (mtp) REVERT: C 556 MET cc_start: 0.7335 (mtm) cc_final: 0.6916 (mtp) outliers start: 21 outliers final: 13 residues processed: 180 average time/residue: 0.2285 time to fit residues: 61.4535 Evaluate side-chains 173 residues out of total 1325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 160 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 584 SER Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 621 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 0 optimal weight: 50.0000 chunk 77 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 423 ASN ** C 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12509 Z= 0.214 Angle : 0.467 8.701 17039 Z= 0.240 Chirality : 0.037 0.154 1974 Planarity : 0.004 0.045 2069 Dihedral : 7.047 126.194 1716 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.69 % Allowed : 10.81 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.21), residues: 1579 helix: 2.30 (0.14), residues: 1298 sheet: None (None), residues: 0 loop : -0.87 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 178 HIS 0.002 0.001 HIS A 367 PHE 0.018 0.001 PHE B 546 TYR 0.008 0.001 TYR A 564 ARG 0.002 0.000 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 171 time to evaluate : 1.349 Fit side-chains REVERT: A 284 LYS cc_start: 0.8602 (mttm) cc_final: 0.8014 (mmtt) REVERT: A 564 TYR cc_start: 0.8580 (m-80) cc_final: 0.8238 (m-80) REVERT: B 248 LEU cc_start: 0.8374 (tp) cc_final: 0.7783 (mp) REVERT: B 355 ARG cc_start: 0.8077 (tmm-80) cc_final: 0.7743 (ttm170) REVERT: B 357 TYR cc_start: 0.7723 (m-80) cc_final: 0.7361 (m-80) REVERT: B 482 ASP cc_start: 0.8744 (t0) cc_final: 0.8466 (t0) REVERT: B 584 SER cc_start: 0.8105 (OUTLIER) cc_final: 0.7841 (p) REVERT: C 502 MET cc_start: 0.7377 (mmp) cc_final: 0.6545 (mtp) REVERT: C 556 MET cc_start: 0.7388 (mtm) cc_final: 0.6924 (mtp) outliers start: 21 outliers final: 15 residues processed: 184 average time/residue: 0.2256 time to fit residues: 61.9878 Evaluate side-chains 184 residues out of total 1325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 168 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 584 SER Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 621 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN B 342 ASN B 552 GLN C 423 ASN C 571 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12509 Z= 0.187 Angle : 0.447 7.623 17039 Z= 0.229 Chirality : 0.036 0.149 1974 Planarity : 0.004 0.045 2069 Dihedral : 6.851 125.684 1716 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.18 % Allowed : 10.48 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.74 (0.21), residues: 1579 helix: 2.36 (0.14), residues: 1297 sheet: None (None), residues: 0 loop : -0.85 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 178 HIS 0.002 0.000 HIS C 394 PHE 0.019 0.001 PHE C 146 TYR 0.007 0.001 TYR A 564 ARG 0.004 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 172 time to evaluate : 1.381 Fit side-chains REVERT: A 163 ARG cc_start: 0.7364 (tmm-80) cc_final: 0.6701 (ttp80) REVERT: A 284 LYS cc_start: 0.8609 (mttm) cc_final: 0.8018 (mmtt) REVERT: B 248 LEU cc_start: 0.8250 (tp) cc_final: 0.7752 (mp) REVERT: B 355 ARG cc_start: 0.7979 (tmm-80) cc_final: 0.7677 (ttm170) REVERT: B 357 TYR cc_start: 0.7712 (m-80) cc_final: 0.7333 (m-80) REVERT: B 584 SER cc_start: 0.8117 (OUTLIER) cc_final: 0.7890 (p) REVERT: C 502 MET cc_start: 0.7372 (mmp) cc_final: 0.6560 (mtp) REVERT: C 556 MET cc_start: 0.7387 (mtm) cc_final: 0.6973 (mtp) outliers start: 27 outliers final: 20 residues processed: 188 average time/residue: 0.2417 time to fit residues: 67.9577 Evaluate side-chains 190 residues out of total 1325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 169 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 584 SER Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 621 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 128 optimal weight: 0.9980 chunk 85 optimal weight: 0.2980 chunk 152 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 423 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12509 Z= 0.164 Angle : 0.439 7.155 17039 Z= 0.225 Chirality : 0.036 0.144 1974 Planarity : 0.004 0.045 2069 Dihedral : 6.672 123.124 1716 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.94 % Allowed : 11.05 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.85 (0.22), residues: 1579 helix: 2.45 (0.15), residues: 1292 sheet: None (None), residues: 0 loop : -0.88 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 150 HIS 0.002 0.000 HIS C 394 PHE 0.031 0.001 PHE A 146 TYR 0.006 0.001 TYR C 157 ARG 0.006 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 173 time to evaluate : 1.158 Fit side-chains REVERT: A 163 ARG cc_start: 0.7381 (tmm-80) cc_final: 0.6693 (ttp80) REVERT: A 284 LYS cc_start: 0.8612 (mttm) cc_final: 0.8023 (mmtt) REVERT: A 564 TYR cc_start: 0.8499 (m-80) cc_final: 0.8163 (m-80) REVERT: B 160 GLN cc_start: 0.6700 (mp10) cc_final: 0.6428 (tp40) REVERT: B 248 LEU cc_start: 0.8230 (tp) cc_final: 0.7730 (mp) REVERT: B 355 ARG cc_start: 0.7987 (tmm-80) cc_final: 0.7695 (ttm170) REVERT: B 357 TYR cc_start: 0.7694 (m-80) cc_final: 0.7360 (m-80) REVERT: B 482 ASP cc_start: 0.8716 (t0) cc_final: 0.8452 (t0) REVERT: C 329 MET cc_start: 0.8708 (mtt) cc_final: 0.8467 (mtp) REVERT: C 502 MET cc_start: 0.7355 (mmp) cc_final: 0.6549 (mtp) REVERT: C 556 MET cc_start: 0.7396 (mtm) cc_final: 0.6975 (mtp) outliers start: 24 outliers final: 19 residues processed: 187 average time/residue: 0.2231 time to fit residues: 62.4524 Evaluate side-chains 188 residues out of total 1325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 169 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 413 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 552 GLN C 347 GLN C 423 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12509 Z= 0.167 Angle : 0.445 9.419 17039 Z= 0.226 Chirality : 0.036 0.152 1974 Planarity : 0.004 0.045 2069 Dihedral : 6.596 121.384 1716 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.94 % Allowed : 11.37 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.22), residues: 1579 helix: 2.46 (0.15), residues: 1292 sheet: None (None), residues: 0 loop : -0.87 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 178 HIS 0.002 0.000 HIS C 394 PHE 0.021 0.001 PHE C 146 TYR 0.006 0.001 TYR A 564 ARG 0.006 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 172 time to evaluate : 1.284 Fit side-chains REVERT: A 163 ARG cc_start: 0.7435 (tmm-80) cc_final: 0.6743 (ttp80) REVERT: A 284 LYS cc_start: 0.8618 (mttm) cc_final: 0.8037 (mmtt) REVERT: A 564 TYR cc_start: 0.8508 (m-80) cc_final: 0.8185 (m-80) REVERT: B 160 GLN cc_start: 0.6691 (mp10) cc_final: 0.6422 (tp40) REVERT: B 248 LEU cc_start: 0.8224 (tp) cc_final: 0.7724 (mp) REVERT: B 355 ARG cc_start: 0.7987 (tmm-80) cc_final: 0.7708 (ttm170) REVERT: B 357 TYR cc_start: 0.7691 (m-80) cc_final: 0.7358 (m-80) REVERT: B 482 ASP cc_start: 0.8822 (t0) cc_final: 0.8487 (t0) REVERT: B 585 MET cc_start: 0.7891 (ttm) cc_final: 0.7685 (ttm) REVERT: C 502 MET cc_start: 0.7434 (mmp) cc_final: 0.6560 (mtp) REVERT: C 556 MET cc_start: 0.7381 (mtm) cc_final: 0.6963 (mtp) outliers start: 24 outliers final: 21 residues processed: 187 average time/residue: 0.2214 time to fit residues: 61.5035 Evaluate side-chains 190 residues out of total 1325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 169 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 413 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 0.9980 chunk 133 optimal weight: 0.0010 chunk 141 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 134 optimal weight: 0.5980 chunk 93 optimal weight: 0.0980 chunk 150 optimal weight: 2.9990 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 423 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12509 Z= 0.133 Angle : 0.425 9.557 17039 Z= 0.215 Chirality : 0.035 0.143 1974 Planarity : 0.004 0.045 2069 Dihedral : 6.418 117.994 1716 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.53 % Allowed : 12.26 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.10 (0.22), residues: 1579 helix: 2.66 (0.15), residues: 1284 sheet: None (None), residues: 0 loop : -0.86 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 178 HIS 0.001 0.000 HIS C 394 PHE 0.019 0.001 PHE C 146 TYR 0.006 0.001 TYR C 157 ARG 0.006 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 174 time to evaluate : 1.389 Fit side-chains REVERT: A 163 ARG cc_start: 0.7455 (tmm-80) cc_final: 0.6743 (ttp80) REVERT: A 284 LYS cc_start: 0.8621 (mttm) cc_final: 0.8046 (mmtt) REVERT: A 480 MET cc_start: 0.6412 (ttm) cc_final: 0.6092 (ttm) REVERT: A 564 TYR cc_start: 0.8444 (m-80) cc_final: 0.8166 (m-80) REVERT: B 160 GLN cc_start: 0.6704 (mp10) cc_final: 0.6441 (tp40) REVERT: B 248 LEU cc_start: 0.8175 (tp) cc_final: 0.7654 (mp) REVERT: B 357 TYR cc_start: 0.7706 (m-80) cc_final: 0.7375 (m-80) REVERT: B 482 ASP cc_start: 0.8797 (t0) cc_final: 0.8525 (t0) REVERT: C 329 MET cc_start: 0.8621 (mtt) cc_final: 0.8104 (mtt) REVERT: C 502 MET cc_start: 0.7411 (mmp) cc_final: 0.6550 (mtp) outliers start: 19 outliers final: 16 residues processed: 186 average time/residue: 0.2301 time to fit residues: 63.5535 Evaluate side-chains 185 residues out of total 1325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 169 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain C residue 413 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 157 optimal weight: 0.7980 chunk 144 optimal weight: 0.0470 chunk 125 optimal weight: 0.5980 chunk 13 optimal weight: 0.1980 chunk 96 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 99 optimal weight: 0.6980 chunk 133 optimal weight: 0.0470 overall best weight: 0.3176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 347 GLN C 423 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12509 Z= 0.122 Angle : 0.422 9.730 17039 Z= 0.211 Chirality : 0.035 0.140 1974 Planarity : 0.004 0.046 2069 Dihedral : 6.185 112.000 1716 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.13 % Allowed : 12.58 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.33 (0.22), residues: 1579 helix: 2.84 (0.15), residues: 1279 sheet: None (None), residues: 0 loop : -0.81 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 178 HIS 0.001 0.000 HIS A 394 PHE 0.019 0.001 PHE C 146 TYR 0.005 0.001 TYR A 157 ARG 0.007 0.000 ARG A 133 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 179 time to evaluate : 1.380 Fit side-chains REVERT: A 133 ARG cc_start: 0.7316 (ttp80) cc_final: 0.6907 (ttp80) REVERT: A 163 ARG cc_start: 0.7445 (tmm-80) cc_final: 0.6706 (ttp80) REVERT: A 284 LYS cc_start: 0.8617 (mttm) cc_final: 0.8068 (mmtt) REVERT: A 480 MET cc_start: 0.6272 (ttm) cc_final: 0.5967 (ttm) REVERT: B 248 LEU cc_start: 0.8191 (tp) cc_final: 0.7654 (mp) REVERT: B 357 TYR cc_start: 0.7669 (m-80) cc_final: 0.7375 (m-80) REVERT: B 485 GLN cc_start: 0.8060 (mp10) cc_final: 0.7483 (mp10) REVERT: B 617 MET cc_start: 0.8740 (ttp) cc_final: 0.8532 (ttm) REVERT: C 329 MET cc_start: 0.8534 (mtt) cc_final: 0.7982 (mtt) REVERT: C 502 MET cc_start: 0.7325 (mmp) cc_final: 0.6495 (mtm) outliers start: 14 outliers final: 8 residues processed: 189 average time/residue: 0.2277 time to fit residues: 63.9705 Evaluate side-chains 179 residues out of total 1325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 171 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain C residue 413 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 0.0370 chunk 115 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 34 optimal weight: 5.9990 chunk 125 optimal weight: 0.7980 chunk 52 optimal weight: 10.0000 chunk 128 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 423 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.164724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.135746 restraints weight = 14170.783| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.28 r_work: 0.3386 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12509 Z= 0.147 Angle : 0.438 9.694 17039 Z= 0.221 Chirality : 0.035 0.147 1974 Planarity : 0.004 0.043 2069 Dihedral : 6.044 108.234 1711 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.65 % Allowed : 13.31 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.24 (0.22), residues: 1579 helix: 2.76 (0.15), residues: 1284 sheet: None (None), residues: 0 loop : -0.80 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 178 HIS 0.001 0.000 HIS C 394 PHE 0.025 0.001 PHE B 138 TYR 0.007 0.001 TYR A 157 ARG 0.006 0.000 ARG A 133 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2578.08 seconds wall clock time: 47 minutes 56.63 seconds (2876.63 seconds total)