Starting phenix.real_space_refine on Tue Feb 13 07:56:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnh_34913/02_2024/8hnh_34913_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnh_34913/02_2024/8hnh_34913.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnh_34913/02_2024/8hnh_34913_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnh_34913/02_2024/8hnh_34913_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnh_34913/02_2024/8hnh_34913_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnh_34913/02_2024/8hnh_34913.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnh_34913/02_2024/8hnh_34913.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnh_34913/02_2024/8hnh_34913_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnh_34913/02_2024/8hnh_34913_updated.pdb" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.041 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: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 2797 2.51 5 N 668 2.21 5 O 737 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 57": "NH1" <-> "NH2" Residue "A ARG 58": "NH1" <-> "NH2" Residue "A GLU 74": "OE1" <-> "OE2" Residue "A ARG 93": "NH1" <-> "NH2" Residue "A TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 181": "NH1" <-> "NH2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 452": "NH1" <-> "NH2" Residue "A TYR 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 526": "NH1" <-> "NH2" Residue "A ARG 532": "NH1" <-> "NH2" Residue "A ARG 580": "NH1" <-> "NH2" Residue "A ARG 614": "NH1" <-> "NH2" Residue "A ARG 623": "NH1" <-> "NH2" Residue "A ARG 633": "NH1" <-> "NH2" Residue "A TYR 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 645": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 4236 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4142 Classifications: {'peptide': 563} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 20, 'TRANS': 542} Chain breaks: 3 Unresolved non-hydrogen bonds: 245 Unresolved non-hydrogen angles: 312 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 10, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 133 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {'30B': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.12, per 1000 atoms: 0.74 Number of scatterers: 4236 At special positions: 0 Unit cell: (56.576, 98.176, 84.032, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 737 8.00 N 668 7.00 C 2797 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 463 " distance=2.03 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 530 " distance=2.03 Simple disulfide: pdb=" SG CYS A 459 " - pdb=" SG CYS A 506 " distance=2.04 Simple disulfide: pdb=" SG CYS A 465 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 524 " distance=2.03 Simple disulfide: pdb=" SG CYS A 489 " - pdb=" SG CYS A 504 " distance=2.03 Simple disulfide: pdb=" SG CYS A 599 " - pdb=" SG CYS A 613 " distance=2.03 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A 802 " - " ASN A 516 " " NAG B 1 " - " ASN A 503 " Time building additional restraints: 1.90 Conformation dependent library (CDL) restraints added in 808.2 milliseconds 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1022 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 17 helices and 1 sheets defined 66.8% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 26 through 59 removed outlier: 3.529A pdb=" N THR A 42 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 46 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 47 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET A 48 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ILE A 53 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE A 59 " --> pdb=" O GLU A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 90 removed outlier: 3.645A pdb=" N GLY A 67 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE A 68 " --> pdb=" O SER A 64 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N PHE A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR A 86 " --> pdb=" O VAL A 82 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LYS A 90 " --> pdb=" O TYR A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 117 removed outlier: 3.550A pdb=" N ALA A 112 " --> pdb=" O GLY A 108 " (cutoff:3.500A) Proline residue: A 114 - end of helix Processing helix chain 'A' and resid 157 through 165 Processing helix chain 'A' and resid 170 through 199 removed outlier: 3.501A pdb=" N VAL A 174 " --> pdb=" O TRP A 171 " (cutoff:3.500A) Proline residue: A 187 - end of helix Proline residue: A 190 - end of helix removed outlier: 3.874A pdb=" N LEU A 193 " --> pdb=" O PRO A 190 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER A 194 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP A 198 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE A 199 " --> pdb=" O ILE A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 232 removed outlier: 4.049A pdb=" N ILE A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLY A 219 " --> pdb=" O ILE A 215 " (cutoff:3.500A) Proline residue: A 220 - end of helix Processing helix chain 'A' and resid 258 through 278 removed outlier: 3.817A pdb=" N SER A 265 " --> pdb=" O ASN A 261 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE A 274 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Proline residue: A 275 - end of helix removed outlier: 4.301A pdb=" N PHE A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 332 Processing helix chain 'A' and resid 336 through 367 removed outlier: 3.564A pdb=" N MET A 340 " --> pdb=" O PRO A 336 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N PHE A 360 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N LYS A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 399 removed outlier: 4.205A pdb=" N ILE A 376 " --> pdb=" O SER A 372 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N VAL A 380 " --> pdb=" O ILE A 376 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE A 383 " --> pdb=" O GLY A 379 " (cutoff:3.500A) Proline residue: A 384 - end of helix Processing helix chain 'A' and resid 404 through 426 removed outlier: 3.874A pdb=" N TYR A 425 " --> pdb=" O PHE A 421 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N PHE A 426 " --> pdb=" O TYR A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 462 Processing helix chain 'A' and resid 484 through 487 No H-bonds generated for 'chain 'A' and resid 484 through 487' Processing helix chain 'A' and resid 528 through 562 removed outlier: 3.655A pdb=" N ARG A 532 " --> pdb=" O ASP A 528 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE A 536 " --> pdb=" O ARG A 532 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY A 551 " --> pdb=" O PHE A 547 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N SER A 554 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N HIS A 555 " --> pdb=" O GLY A 551 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL A 556 " --> pdb=" O GLY A 552 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL A 560 " --> pdb=" O VAL A 556 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS A 561 " --> pdb=" O MET A 557 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 582 removed outlier: 3.738A pdb=" N LYS A 568 " --> pdb=" O PRO A 565 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N SER A 569 " --> pdb=" O GLU A 566 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 572 " --> pdb=" O SER A 569 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 581 " --> pdb=" O VAL A 578 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU A 582 " --> pdb=" O ILE A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 598 removed outlier: 4.052A pdb=" N THR A 597 " --> pdb=" O ALA A 593 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR A 598 " --> pdb=" O LEU A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 650 Processing sheet with id= A, first strand: chain 'A' and resid 473 through 475 242 hydrogen bonds defined for protein. 573 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: 0.88 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 626 1.31 - 1.44: 1242 1.44 - 1.56: 2422 1.56 - 1.69: 2 1.69 - 1.81: 51 Bond restraints: 4343 Sorted by residual: bond pdb=" C18 30B A 801 " pdb=" C22 30B A 801 " ideal model delta sigma weight residual 1.578 1.321 0.257 2.00e-02 2.50e+03 1.65e+02 bond pdb=" C36 30B A 801 " pdb=" S35 30B A 801 " ideal model delta sigma weight residual 1.519 1.731 -0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C34 30B A 801 " pdb=" S35 30B A 801 " ideal model delta sigma weight residual 1.546 1.744 -0.198 2.00e-02 2.50e+03 9.80e+01 bond pdb=" C37 30B A 801 " pdb=" N38 30B A 801 " ideal model delta sigma weight residual 1.567 1.372 0.195 2.00e-02 2.50e+03 9.48e+01 bond pdb=" C3 30B A 801 " pdb=" C4 30B A 801 " ideal model delta sigma weight residual 1.667 1.512 0.155 2.00e-02 2.50e+03 6.02e+01 ... (remaining 4338 not shown) Histogram of bond angle deviations from ideal: 59.68 - 74.67: 6 74.67 - 89.66: 0 89.66 - 104.66: 81 104.66 - 119.65: 3567 119.65 - 134.64: 2252 Bond angle restraints: 5906 Sorted by residual: angle pdb=" C16 30B A 801 " pdb=" N8 30B A 801 " pdb=" C6 30B A 801 " ideal model delta sigma weight residual 109.55 131.67 -22.12 3.00e+00 1.11e-01 5.44e+01 angle pdb=" N TYR A 338 " pdb=" CA TYR A 338 " pdb=" C TYR A 338 " ideal model delta sigma weight residual 111.36 119.22 -7.86 1.09e+00 8.42e-01 5.19e+01 angle pdb=" C17 30B A 801 " pdb=" C11 30B A 801 " pdb=" C18 30B A 801 " ideal model delta sigma weight residual 141.15 120.58 20.57 3.00e+00 1.11e-01 4.70e+01 angle pdb=" N THR A 382 " pdb=" CA THR A 382 " pdb=" C THR A 382 " ideal model delta sigma weight residual 111.28 118.46 -7.18 1.09e+00 8.42e-01 4.34e+01 angle pdb=" N ILE A 585 " pdb=" CA ILE A 585 " pdb=" C ILE A 585 " ideal model delta sigma weight residual 111.56 117.20 -5.64 8.60e-01 1.35e+00 4.30e+01 ... (remaining 5901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.05: 2461 30.05 - 60.10: 67 60.10 - 90.15: 12 90.15 - 120.20: 5 120.20 - 150.26: 2 Dihedral angle restraints: 2547 sinusoidal: 940 harmonic: 1607 Sorted by residual: dihedral pdb=" CB CYS A 142 " pdb=" SG CYS A 142 " pdb=" SG CYS A 463 " pdb=" CB CYS A 463 " ideal model delta sinusoidal sigma weight residual -86.00 -127.20 41.20 1 1.00e+01 1.00e-02 2.38e+01 dihedral pdb=" CB CYS A 430 " pdb=" SG CYS A 430 " pdb=" SG CYS A 530 " pdb=" CB CYS A 530 " ideal model delta sinusoidal sigma weight residual 93.00 132.66 -39.66 1 1.00e+01 1.00e-02 2.21e+01 dihedral pdb=" C20 30B A 801 " pdb=" C14 30B A 801 " pdb=" C19 30B A 801 " pdb=" N13 30B A 801 " ideal model delta sinusoidal sigma weight residual 90.78 -59.48 150.26 1 3.00e+01 1.11e-03 1.99e+01 ... (remaining 2544 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.986: 689 0.986 - 1.973: 1 1.973 - 2.959: 0 2.959 - 3.945: 0 3.945 - 4.932: 1 Chirality restraints: 691 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.66 -0.74 2.00e-02 2.50e+03 1.37e+03 chirality pdb=" C5 30B A 801 " pdb=" C1 30B A 801 " pdb=" C4 30B A 801 " pdb=" O23 30B A 801 " both_signs ideal model delta sigma weight residual False 2.50 -2.43 4.93 2.00e-01 2.50e+01 6.08e+02 chirality pdb=" C1 NAG A 802 " pdb=" ND2 ASN A 516 " pdb=" C2 NAG A 802 " pdb=" O5 NAG A 802 " both_signs ideal model delta sigma weight residual False -2.40 -0.88 -1.52 2.00e-01 2.50e+01 5.81e+01 ... (remaining 688 not shown) Planarity restraints: 720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " 0.313 2.00e-02 2.50e+03 2.66e-01 8.82e+02 pdb=" C7 NAG B 2 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " 0.181 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " -0.463 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 503 " -0.232 2.00e-02 2.50e+03 2.47e-01 7.64e+02 pdb=" CG ASN A 503 " 0.085 2.00e-02 2.50e+03 pdb=" OD1 ASN A 503 " 0.096 2.00e-02 2.50e+03 pdb=" ND2 ASN A 503 " 0.368 2.00e-02 2.50e+03 pdb=" C1 NAG B 1 " -0.317 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " -0.164 2.00e-02 2.50e+03 1.39e-01 2.41e+02 pdb=" C7 NAG B 1 " 0.032 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " 0.037 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " 0.224 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " -0.129 2.00e-02 2.50e+03 ... (remaining 717 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 564 2.75 - 3.28: 4746 3.28 - 3.82: 6567 3.82 - 4.36: 7648 4.36 - 4.90: 12970 Nonbonded interactions: 32495 Sorted by model distance: nonbonded pdb=" CE1 PHE A 116 " pdb=" CZ3 TRP A 259 " model vdw 2.207 3.640 nonbonded pdb=" CE1 PHE A 116 " pdb=" CE3 TRP A 259 " model vdw 2.218 3.640 nonbonded pdb=" NH1 ARG A 57 " pdb=" O SER A 252 " model vdw 2.219 2.520 nonbonded pdb=" OE1 GLN A 366 " pdb=" OG SER A 618 " model vdw 2.291 2.440 nonbonded pdb=" CZ PHE A 116 " pdb=" CE3 TRP A 259 " model vdw 2.422 3.640 ... (remaining 32490 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.690 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 16.870 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:3.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 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 : 0.012 0.257 4343 Z= 0.809 Angle : 1.523 22.124 5906 Z= 0.959 Chirality : 0.217 4.932 691 Planarity : 0.015 0.266 718 Dihedral : 15.982 150.256 1504 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.67 % Allowed : 14.91 % Favored : 81.42 % Cbeta Deviations : 0.39 % 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: 1.75 (0.33), residues: 555 helix: 2.38 (0.27), residues: 327 sheet: None (None), residues: 0 loop : -0.69 (0.33), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 259 HIS 0.005 0.001 HIS A 555 PHE 0.020 0.002 PHE A 341 TYR 0.025 0.002 TYR A 590 ARG 0.003 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 88 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 345 THR cc_start: 0.8029 (t) cc_final: 0.6892 (p) REVERT: A 648 LYS cc_start: 0.8875 (ttpt) cc_final: 0.8482 (ttpp) outliers start: 15 outliers final: 7 residues processed: 100 average time/residue: 0.1720 time to fit residues: 21.4977 Evaluate side-chains 77 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 70 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 639 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 0.5980 chunk 42 optimal weight: 30.0000 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 22 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 GLN A 564 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4343 Z= 0.256 Angle : 0.826 16.827 5906 Z= 0.372 Chirality : 0.055 0.635 691 Planarity : 0.006 0.059 718 Dihedral : 13.480 144.445 692 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.93 % Allowed : 19.07 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.33), residues: 555 helix: 1.58 (0.26), residues: 345 sheet: None (None), residues: 0 loop : -0.47 (0.37), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 171 HIS 0.003 0.001 HIS A 54 PHE 0.016 0.002 PHE A 73 TYR 0.015 0.002 TYR A 121 ARG 0.002 0.001 ARG A 93 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.7592 (mt) cc_final: 0.6897 (tt) REVERT: A 648 LYS cc_start: 0.8723 (ttpt) cc_final: 0.8417 (ttpp) outliers start: 12 outliers final: 8 residues processed: 72 average time/residue: 0.1893 time to fit residues: 16.9277 Evaluate side-chains 66 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 58 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 34 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 50 optimal weight: 0.2980 chunk 55 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 17 optimal weight: 0.0770 chunk 40 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4343 Z= 0.204 Angle : 0.725 15.766 5906 Z= 0.326 Chirality : 0.052 0.619 691 Planarity : 0.005 0.051 718 Dihedral : 12.022 149.322 687 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.67 % Allowed : 18.34 % Favored : 78.00 % 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: 0.95 (0.34), residues: 555 helix: 1.29 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -0.45 (0.38), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 171 HIS 0.002 0.001 HIS A 54 PHE 0.012 0.001 PHE A 73 TYR 0.020 0.001 TYR A 590 ARG 0.002 0.000 ARG A 57 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 61 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.7635 (mt) cc_final: 0.6847 (tt) REVERT: A 46 ILE cc_start: 0.7872 (OUTLIER) cc_final: 0.7449 (tp) REVERT: A 111 THR cc_start: 0.7325 (m) cc_final: 0.7040 (m) REVERT: A 113 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8248 (tp) REVERT: A 577 MET cc_start: 0.7504 (ttp) cc_final: 0.7126 (ttt) REVERT: A 648 LYS cc_start: 0.8611 (ttpt) cc_final: 0.8340 (ttpp) outliers start: 15 outliers final: 7 residues processed: 72 average time/residue: 0.1897 time to fit residues: 16.9579 Evaluate side-chains 70 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 61 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 24 optimal weight: 0.4980 chunk 34 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 14 optimal weight: 0.0870 chunk 45 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4343 Z= 0.207 Angle : 0.695 14.348 5906 Z= 0.306 Chirality : 0.049 0.533 691 Planarity : 0.005 0.050 718 Dihedral : 12.025 154.161 683 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.69 % Allowed : 19.32 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.34), residues: 555 helix: 1.27 (0.27), residues: 349 sheet: None (None), residues: 0 loop : -0.44 (0.37), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 171 HIS 0.003 0.001 HIS A 54 PHE 0.011 0.001 PHE A 73 TYR 0.020 0.001 TYR A 590 ARG 0.002 0.000 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 62 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: A 31 LEU cc_start: 0.7620 (mt) cc_final: 0.6859 (tt) REVERT: A 46 ILE cc_start: 0.7824 (OUTLIER) cc_final: 0.7353 (tp) REVERT: A 78 LEU cc_start: 0.8297 (mm) cc_final: 0.7945 (mt) REVERT: A 532 ARG cc_start: 0.6594 (tpp-160) cc_final: 0.6277 (mmt180) REVERT: A 591 PHE cc_start: 0.7744 (OUTLIER) cc_final: 0.5594 (t80) REVERT: A 648 LYS cc_start: 0.8525 (ttpt) cc_final: 0.8276 (ttpp) outliers start: 11 outliers final: 7 residues processed: 70 average time/residue: 0.1940 time to fit residues: 17.0044 Evaluate side-chains 68 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 59 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 0.0050 chunk 22 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 37 optimal weight: 8.9990 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 31 optimal weight: 0.3980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4343 Z= 0.191 Angle : 0.699 13.584 5906 Z= 0.308 Chirality : 0.048 0.491 691 Planarity : 0.004 0.049 718 Dihedral : 12.189 155.335 683 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 4.16 % Allowed : 18.83 % Favored : 77.02 % 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: 0.91 (0.34), residues: 555 helix: 1.23 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -0.42 (0.37), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 171 HIS 0.002 0.001 HIS A 555 PHE 0.010 0.001 PHE A 262 TYR 0.020 0.001 TYR A 590 ARG 0.002 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 54 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.7630 (mt) cc_final: 0.6866 (tt) REVERT: A 46 ILE cc_start: 0.7814 (OUTLIER) cc_final: 0.7411 (tp) REVERT: A 267 LEU cc_start: 0.6572 (OUTLIER) cc_final: 0.5886 (tt) REVERT: A 532 ARG cc_start: 0.6470 (tpp-160) cc_final: 0.6249 (mmt180) REVERT: A 591 PHE cc_start: 0.7705 (OUTLIER) cc_final: 0.5699 (t80) REVERT: A 648 LYS cc_start: 0.8467 (ttpt) cc_final: 0.8201 (ttpp) outliers start: 17 outliers final: 9 residues processed: 66 average time/residue: 0.1921 time to fit residues: 15.7408 Evaluate side-chains 66 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 54 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 0.4980 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 28 optimal weight: 0.0050 chunk 52 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4343 Z= 0.187 Angle : 0.668 12.590 5906 Z= 0.296 Chirality : 0.047 0.439 691 Planarity : 0.004 0.048 718 Dihedral : 11.870 155.604 683 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.91 % Allowed : 20.54 % Favored : 75.55 % 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: 0.93 (0.34), residues: 555 helix: 1.26 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -0.44 (0.38), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 171 HIS 0.003 0.001 HIS A 54 PHE 0.009 0.001 PHE A 73 TYR 0.019 0.001 TYR A 590 ARG 0.002 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 57 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.7619 (mt) cc_final: 0.6878 (tt) REVERT: A 46 ILE cc_start: 0.7760 (OUTLIER) cc_final: 0.7336 (tp) REVERT: A 267 LEU cc_start: 0.6499 (OUTLIER) cc_final: 0.5836 (tt) REVERT: A 532 ARG cc_start: 0.6387 (tpp-160) cc_final: 0.6166 (mmt180) REVERT: A 591 PHE cc_start: 0.7670 (OUTLIER) cc_final: 0.5945 (t80) REVERT: A 648 LYS cc_start: 0.8384 (ttpt) cc_final: 0.8141 (ttpp) outliers start: 16 outliers final: 12 residues processed: 70 average time/residue: 0.1954 time to fit residues: 17.0023 Evaluate side-chains 71 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 56 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 34 optimal weight: 0.0070 chunk 36 optimal weight: 1.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4343 Z= 0.198 Angle : 0.668 12.106 5906 Z= 0.295 Chirality : 0.046 0.416 691 Planarity : 0.004 0.050 718 Dihedral : 11.913 155.314 683 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.91 % Allowed : 21.76 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.34), residues: 555 helix: 1.25 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -0.39 (0.38), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 254 HIS 0.002 0.001 HIS A 575 PHE 0.011 0.001 PHE A 117 TYR 0.024 0.001 TYR A 590 ARG 0.002 0.000 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 56 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.7596 (mt) cc_final: 0.6859 (tt) REVERT: A 46 ILE cc_start: 0.7795 (OUTLIER) cc_final: 0.7406 (tp) REVERT: A 648 LYS cc_start: 0.8323 (ttpt) cc_final: 0.8060 (tttm) outliers start: 16 outliers final: 13 residues processed: 69 average time/residue: 0.1962 time to fit residues: 16.7708 Evaluate side-chains 71 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 57 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 42 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 0.2980 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4343 Z= 0.236 Angle : 0.681 11.738 5906 Z= 0.304 Chirality : 0.046 0.403 691 Planarity : 0.005 0.051 718 Dihedral : 11.973 153.975 683 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.67 % Allowed : 22.98 % Favored : 73.35 % 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: 0.80 (0.34), residues: 555 helix: 1.10 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -0.37 (0.38), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 254 HIS 0.003 0.001 HIS A 575 PHE 0.009 0.001 PHE A 73 TYR 0.023 0.001 TYR A 590 ARG 0.007 0.001 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 62 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.7612 (mt) cc_final: 0.6904 (tt) REVERT: A 46 ILE cc_start: 0.7752 (OUTLIER) cc_final: 0.7324 (tp) REVERT: A 79 LEU cc_start: 0.8109 (mt) cc_final: 0.7839 (tp) REVERT: A 648 LYS cc_start: 0.8294 (ttpt) cc_final: 0.8035 (tttm) outliers start: 15 outliers final: 14 residues processed: 74 average time/residue: 0.1844 time to fit residues: 17.1485 Evaluate side-chains 76 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 61 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.8980 chunk 47 optimal weight: 0.0670 chunk 50 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 36 optimal weight: 0.0870 chunk 55 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4343 Z= 0.178 Angle : 0.657 11.506 5906 Z= 0.290 Chirality : 0.044 0.386 691 Planarity : 0.004 0.050 718 Dihedral : 11.901 155.124 683 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.67 % Allowed : 23.23 % Favored : 73.11 % 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: 0.94 (0.34), residues: 555 helix: 1.17 (0.27), residues: 355 sheet: None (None), residues: 0 loop : -0.25 (0.39), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 171 HIS 0.002 0.001 HIS A 555 PHE 0.008 0.001 PHE A 73 TYR 0.023 0.001 TYR A 590 ARG 0.006 0.001 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 62 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.7642 (mt) cc_final: 0.6956 (tt) REVERT: A 46 ILE cc_start: 0.7770 (OUTLIER) cc_final: 0.7390 (tp) outliers start: 15 outliers final: 13 residues processed: 75 average time/residue: 0.1686 time to fit residues: 15.9706 Evaluate side-chains 71 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 57 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 0.7980 chunk 34 optimal weight: 0.3980 chunk 27 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 13 optimal weight: 0.0030 chunk 40 optimal weight: 0.0980 chunk 6 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4343 Z= 0.172 Angle : 0.650 11.059 5906 Z= 0.290 Chirality : 0.045 0.364 691 Planarity : 0.004 0.049 718 Dihedral : 11.876 154.593 683 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.18 % Allowed : 22.98 % Favored : 73.84 % 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: 0.97 (0.34), residues: 555 helix: 1.18 (0.27), residues: 354 sheet: None (None), residues: 0 loop : -0.19 (0.39), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 171 HIS 0.002 0.001 HIS A 54 PHE 0.008 0.001 PHE A 175 TYR 0.022 0.001 TYR A 590 ARG 0.007 0.001 ARG A 181 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 58 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.7680 (mt) cc_final: 0.6975 (tt) REVERT: A 46 ILE cc_start: 0.7754 (OUTLIER) cc_final: 0.7367 (tp) REVERT: A 467 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7379 (mp0) REVERT: A 591 PHE cc_start: 0.7551 (OUTLIER) cc_final: 0.6116 (t80) outliers start: 13 outliers final: 10 residues processed: 69 average time/residue: 0.1722 time to fit residues: 15.2088 Evaluate side-chains 67 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 54 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 39 optimal weight: 0.0570 chunk 2 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 0.0980 chunk 29 optimal weight: 0.0770 chunk 38 optimal weight: 0.0980 chunk 1 optimal weight: 0.6980 chunk 35 optimal weight: 0.2980 overall best weight: 0.1256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.241510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.206364 restraints weight = 4013.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.204893 restraints weight = 3980.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.206249 restraints weight = 4154.031| |-----------------------------------------------------------------------------| r_work (final): 0.4369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4343 Z= 0.156 Angle : 0.648 10.668 5906 Z= 0.291 Chirality : 0.044 0.354 691 Planarity : 0.004 0.046 718 Dihedral : 11.908 155.227 683 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.18 % Allowed : 23.96 % Favored : 72.86 % 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: 1.00 (0.34), residues: 555 helix: 1.17 (0.28), residues: 356 sheet: None (None), residues: 0 loop : -0.13 (0.39), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 171 HIS 0.005 0.001 HIS A 54 PHE 0.009 0.001 PHE A 175 TYR 0.022 0.001 TYR A 590 ARG 0.005 0.001 ARG A 181 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1281.89 seconds wall clock time: 23 minutes 55.29 seconds (1435.29 seconds total)