Starting phenix.real_space_refine (version: 1.21rc1) on Mon Oct 2 23:20:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6l_36922/10_2023/8k6l_36922_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6l_36922/10_2023/8k6l_36922.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6l_36922/10_2023/8k6l_36922_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6l_36922/10_2023/8k6l_36922_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6l_36922/10_2023/8k6l_36922_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6l_36922/10_2023/8k6l_36922.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6l_36922/10_2023/8k6l_36922.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6l_36922/10_2023/8k6l_36922_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6l_36922/10_2023/8k6l_36922_updated.pdb" } resolution = 2.92 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= 0.092 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 S 34 5.16 5 Cl 2 4.86 5 C 2749 2.51 5 N 651 2.21 5 O 719 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 56": "OE1" <-> "OE2" Residue "A ARG 58": "NH1" <-> "NH2" Residue "A ASP 70": "OD1" <-> "OD2" Residue "A PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 74": "OE1" <-> "OE2" Residue "A PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 236": "OD1" <-> "OD2" Residue "A ASP 241": "OD1" <-> "OD2" Residue "A PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 527": "OD1" <-> "OD2" Residue "A ASP 528": "OD1" <-> "OD2" Residue "A PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 596": "OD1" <-> "OD2" Residue "A ARG 614": "NH1" <-> "NH2" Residue "A TYR 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 4155 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4086 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 18, 'TRANS': 528} Chain breaks: 3 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 234 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 8, 'ASP:plan': 4, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 109 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 chiralities: 2 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'IOQ': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.79, per 1000 atoms: 0.67 Number of scatterers: 4155 At special positions: 0 Unit cell: (65.24, 100.656, 87.608, 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) Cl 2 17.00 S 34 16.00 O 719 8.00 N 651 7.00 C 2749 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=1.71 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: 1.88 Conformation dependent library (CDL) restraints added in 661.3 milliseconds 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 996 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 19 helices and 0 sheets defined 61.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 27 through 50 removed outlier: 3.725A pdb=" N ALA A 33 " --> pdb=" O MET A 29 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.800A pdb=" N PHE A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLU A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A 75 " --> pdb=" O GLY A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 removed outlier: 3.676A pdb=" N SER A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 117 removed outlier: 3.808A pdb=" N THR A 111 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ALA A 112 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU A 113 " --> pdb=" O VAL A 109 " (cutoff:3.500A) Proline residue: A 114 - end of helix Processing helix chain 'A' and resid 171 through 198 removed outlier: 4.252A pdb=" N THR A 186 " --> pdb=" O GLY A 182 " (cutoff:3.500A) Proline residue: A 187 - end of helix Proline residue: A 190 - end of helix removed outlier: 3.741A pdb=" N SER A 194 " --> pdb=" O PRO A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 232 removed outlier: 4.429A pdb=" N MET A 217 " --> pdb=" O ASN A 213 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ILE A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N GLY A 219 " --> pdb=" O ILE A 215 " (cutoff:3.500A) Proline residue: A 220 - end of helix removed outlier: 3.865A pdb=" N SER A 228 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 273 removed outlier: 3.922A pdb=" N VAL A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER A 265 " --> pdb=" O ASN A 261 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 324 through 333 removed outlier: 3.810A pdb=" N ILE A 332 " --> pdb=" O SER A 328 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 333 " --> pdb=" O PHE A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 366 removed outlier: 5.301A pdb=" N PHE A 360 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LYS A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 400 removed outlier: 3.865A pdb=" N VAL A 380 " --> pdb=" O ILE A 376 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Proline residue: A 384 - end of helix removed outlier: 3.514A pdb=" N ILE A 397 " --> pdb=" O GLY A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 427 removed outlier: 3.876A pdb=" N PHE A 421 " --> pdb=" O MET A 417 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR A 422 " --> pdb=" O SER A 418 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N TYR A 425 " --> pdb=" O PHE A 421 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N PHE A 426 " --> pdb=" O TYR A 422 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N PHE A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 460 No H-bonds generated for 'chain 'A' and resid 458 through 460' Processing helix chain 'A' and resid 528 through 549 removed outlier: 3.542A pdb=" N PHE A 536 " --> pdb=" O ARG A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 559 Processing helix chain 'A' and resid 568 through 582 Processing helix chain 'A' and resid 587 through 598 removed outlier: 4.276A pdb=" N THR A 597 " --> pdb=" O ALA A 593 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N THR A 598 " --> pdb=" O LEU A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 650 210 hydrogen bonds defined for protein. 630 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: 0.96 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 881 1.33 - 1.45: 1009 1.45 - 1.57: 2315 1.57 - 1.70: 0 1.70 - 1.82: 53 Bond restraints: 4258 Sorted by residual: bond pdb=" C16 IOQ A 801 " pdb=" O17 IOQ A 801 " ideal model delta sigma weight residual 1.486 1.367 0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" C18 IOQ A 801 " pdb=" O17 IOQ A 801 " ideal model delta sigma weight residual 1.485 1.369 0.116 2.00e-02 2.50e+03 3.34e+01 bond pdb=" C THR A 186 " pdb=" N PRO A 187 " ideal model delta sigma weight residual 1.331 1.371 -0.039 7.90e-03 1.60e+04 2.44e+01 bond pdb=" C5 IOQ A 801 " pdb=" C7 IOQ A 801 " ideal model delta sigma weight residual 1.550 1.466 0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" C18 IOQ A 801 " pdb=" C23 IOQ A 801 " ideal model delta sigma weight residual 1.341 1.413 -0.072 2.00e-02 2.50e+03 1.30e+01 ... (remaining 4253 not shown) Histogram of bond angle deviations from ideal: 100.27 - 107.02: 112 107.02 - 113.77: 2343 113.77 - 120.51: 1776 120.51 - 127.26: 1513 127.26 - 134.01: 38 Bond angle restraints: 5782 Sorted by residual: angle pdb=" C ILE A 585 " pdb=" CA ILE A 585 " pdb=" CB ILE A 585 " ideal model delta sigma weight residual 111.30 101.87 9.43 9.60e-01 1.09e+00 9.65e+01 angle pdb=" N ILE A 52 " pdb=" CA ILE A 52 " pdb=" C ILE A 52 " ideal model delta sigma weight residual 110.62 117.58 -6.96 1.02e+00 9.61e-01 4.65e+01 angle pdb=" N ASN A 375 " pdb=" CA ASN A 375 " pdb=" C ASN A 375 " ideal model delta sigma weight residual 111.02 120.98 -9.96 1.52e+00 4.33e-01 4.30e+01 angle pdb=" C ALA A 32 " pdb=" N ALA A 33 " pdb=" CA ALA A 33 " ideal model delta sigma weight residual 120.28 129.02 -8.74 1.34e+00 5.57e-01 4.25e+01 angle pdb=" C THR A 186 " pdb=" N PRO A 187 " pdb=" CA PRO A 187 " ideal model delta sigma weight residual 121.00 113.85 7.15 1.16e+00 7.43e-01 3.80e+01 ... (remaining 5777 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 2206 16.82 - 33.64: 169 33.64 - 50.46: 45 50.46 - 67.28: 11 67.28 - 84.10: 4 Dihedral angle restraints: 2435 sinusoidal: 871 harmonic: 1564 Sorted by residual: 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 -86.00 -157.45 71.45 1 1.00e+01 1.00e-02 6.55e+01 dihedral pdb=" CB CYS A 599 " pdb=" SG CYS A 599 " pdb=" SG CYS A 613 " pdb=" CB CYS A 613 " ideal model delta sinusoidal sigma weight residual -86.00 -155.91 69.91 1 1.00e+01 1.00e-02 6.30e+01 dihedral pdb=" C TYR A 590 " pdb=" N TYR A 590 " pdb=" CA TYR A 590 " pdb=" CB TYR A 590 " ideal model delta harmonic sigma weight residual -122.60 -139.33 16.73 0 2.50e+00 1.60e-01 4.48e+01 ... (remaining 2432 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.243: 672 0.243 - 0.486: 2 0.486 - 0.729: 2 0.729 - 0.972: 1 0.972 - 1.215: 1 Chirality restraints: 678 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 -2.19 -0.21 2.00e-02 2.50e+03 1.13e+02 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 503 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.18 -1.22 2.00e-01 2.50e+01 3.69e+01 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 -1.47 -0.93 2.00e-01 2.50e+01 2.16e+01 ... (remaining 675 not shown) Planarity restraints: 702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " -0.339 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C7 NAG B 1 " 0.079 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " -0.094 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " 0.524 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " -0.170 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " -0.310 2.00e-02 2.50e+03 2.61e-01 8.49e+02 pdb=" C7 NAG B 2 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " -0.189 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " 0.448 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 802 " 0.309 2.00e-02 2.50e+03 2.60e-01 8.48e+02 pdb=" C7 NAG A 802 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG A 802 " 0.189 2.00e-02 2.50e+03 pdb=" N2 NAG A 802 " -0.448 2.00e-02 2.50e+03 pdb=" O7 NAG A 802 " 0.030 2.00e-02 2.50e+03 ... (remaining 699 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1281 2.82 - 3.34: 3843 3.34 - 3.86: 6430 3.86 - 4.38: 7227 4.38 - 4.90: 12370 Nonbonded interactions: 31151 Sorted by model distance: nonbonded pdb=" O SER A 85 " pdb=" OG SER A 89 " model vdw 2.297 2.440 nonbonded pdb=" O GLY A 324 " pdb=" OG SER A 328 " model vdw 2.387 2.440 nonbonded pdb=" O LEU A 507 " pdb=" CD1 LEU A 507 " model vdw 2.400 3.460 nonbonded pdb=" O SER A 491 " pdb=" CD1 PHE A 501 " model vdw 2.463 3.340 nonbonded pdb=" O SER A 371 " pdb=" OG SER A 371 " model vdw 2.475 2.440 ... (remaining 31146 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 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: 3.750 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.140 Find NCS groups from input model: 0.110 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:12.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 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 : 0.006 0.119 4258 Z= 0.435 Angle : 1.022 11.983 5782 Z= 0.662 Chirality : 0.087 1.215 678 Planarity : 0.019 0.294 700 Dihedral : 13.507 84.100 1418 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.17 % Allowed : 13.98 % Favored : 83.86 % Cbeta Deviations : 0.20 % 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: -2.44 (0.31), residues: 539 helix: -0.93 (0.25), residues: 333 sheet: None (None), residues: 0 loop : -2.71 (0.36), residues: 206 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 0.487 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 83 average time/residue: 1.0803 time to fit residues: 93.2479 Evaluate side-chains 58 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 55 time to evaluate : 0.468 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.6307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 22 optimal weight: 0.0770 chunk 13 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 31 optimal weight: 0.0060 chunk 49 optimal weight: 4.9990 overall best weight: 0.4754 ------------------------------------------------------------------------------- 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: 0.7782 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4258 Z= 0.183 Angle : 0.620 9.142 5782 Z= 0.313 Chirality : 0.057 0.787 678 Planarity : 0.004 0.045 700 Dihedral : 4.159 23.397 583 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.13 % Allowed : 20.96 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.36), residues: 539 helix: 0.75 (0.28), residues: 342 sheet: None (None), residues: 0 loop : -2.32 (0.39), residues: 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 52 time to evaluate : 0.582 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 62 average time/residue: 1.0500 time to fit residues: 67.9124 Evaluate side-chains 54 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 0.467 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.6319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.0010 chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- 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: 0.7825 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4258 Z= 0.203 Angle : 0.598 9.603 5782 Z= 0.298 Chirality : 0.052 0.660 678 Planarity : 0.004 0.045 700 Dihedral : 4.032 21.577 583 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.13 % Allowed : 20.24 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.37), residues: 539 helix: 1.41 (0.29), residues: 338 sheet: None (None), residues: 0 loop : -1.95 (0.39), residues: 201 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 52 time to evaluate : 0.524 Fit side-chains outliers start: 13 outliers final: 10 residues processed: 63 average time/residue: 0.9964 time to fit residues: 65.7010 Evaluate side-chains 57 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 47 time to evaluate : 0.472 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 1 average time/residue: 0.0887 time to fit residues: 0.7645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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: 0.7904 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4258 Z= 0.263 Angle : 0.610 7.839 5782 Z= 0.311 Chirality : 0.050 0.515 678 Planarity : 0.004 0.043 700 Dihedral : 4.073 19.400 583 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.10 % Allowed : 20.24 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.37), residues: 539 helix: 1.50 (0.29), residues: 338 sheet: None (None), residues: 0 loop : -1.74 (0.40), residues: 201 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 52 time to evaluate : 0.476 Fit side-chains outliers start: 17 outliers final: 10 residues processed: 63 average time/residue: 0.9827 time to fit residues: 64.7582 Evaluate side-chains 59 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 49 time to evaluate : 0.425 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.0583 time to fit residues: 0.7771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 26 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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: 0.7954 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 4258 Z= 0.326 Angle : 0.635 7.830 5782 Z= 0.328 Chirality : 0.051 0.485 678 Planarity : 0.004 0.045 700 Dihedral : 4.230 19.123 583 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 5.54 % Allowed : 20.48 % Favored : 73.98 % 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: 0.52 (0.37), residues: 539 helix: 1.42 (0.29), residues: 338 sheet: None (None), residues: 0 loop : -1.55 (0.41), residues: 201 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 50 time to evaluate : 0.492 Fit side-chains outliers start: 23 outliers final: 13 residues processed: 67 average time/residue: 1.0336 time to fit residues: 72.6278 Evaluate side-chains 62 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 49 time to evaluate : 0.470 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 1 average time/residue: 1.7153 time to fit residues: 2.4220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.0870 chunk 27 optimal weight: 6.9990 chunk 50 optimal weight: 0.0270 chunk 5 optimal weight: 0.5980 overall best weight: 0.5016 ------------------------------------------------------------------------------- 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: 0.7863 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4258 Z= 0.173 Angle : 0.545 7.285 5782 Z= 0.278 Chirality : 0.048 0.458 678 Planarity : 0.004 0.045 700 Dihedral : 3.917 19.128 583 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.61 % Allowed : 23.61 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.37), residues: 539 helix: 1.90 (0.30), residues: 331 sheet: None (None), residues: 0 loop : -1.46 (0.41), residues: 208 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 48 time to evaluate : 0.465 Fit side-chains outliers start: 15 outliers final: 12 residues processed: 60 average time/residue: 1.0232 time to fit residues: 64.2443 Evaluate side-chains 59 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 47 time to evaluate : 0.469 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 0.0855 time to fit residues: 0.7576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 0.0970 chunk 43 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 15 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.7859 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4258 Z= 0.177 Angle : 0.535 7.981 5782 Z= 0.271 Chirality : 0.047 0.440 678 Planarity : 0.004 0.044 700 Dihedral : 3.758 18.038 583 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.61 % Allowed : 22.17 % Favored : 74.22 % 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: 1.26 (0.37), residues: 539 helix: 2.20 (0.30), residues: 325 sheet: None (None), residues: 0 loop : -1.42 (0.40), residues: 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 47 time to evaluate : 0.479 Fit side-chains outliers start: 15 outliers final: 13 residues processed: 59 average time/residue: 0.9984 time to fit residues: 61.8037 Evaluate side-chains 59 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 46 time to evaluate : 0.493 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 3 average time/residue: 0.9694 time to fit residues: 3.6746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 40 optimal weight: 0.0030 chunk 47 optimal weight: 0.4980 chunk 49 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 0.0470 overall best weight: 0.4688 ------------------------------------------------------------------------------- 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: 0.7831 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4258 Z= 0.161 Angle : 0.525 8.335 5782 Z= 0.267 Chirality : 0.046 0.430 678 Planarity : 0.004 0.045 700 Dihedral : 3.644 19.167 583 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.37 % Allowed : 22.65 % Favored : 73.98 % 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: 1.45 (0.37), residues: 539 helix: 2.36 (0.30), residues: 325 sheet: None (None), residues: 0 loop : -1.37 (0.40), residues: 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 48 time to evaluate : 0.480 Fit side-chains outliers start: 14 outliers final: 12 residues processed: 59 average time/residue: 1.0102 time to fit residues: 62.3985 Evaluate side-chains 59 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 47 time to evaluate : 0.464 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 0.0947 time to fit residues: 0.7776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.4980 chunk 43 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 31 optimal weight: 0.0270 chunk 51 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 0.2980 chunk 53 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 overall best weight: 0.4238 ------------------------------------------------------------------------------- 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: 0.7818 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4258 Z= 0.154 Angle : 0.516 8.607 5782 Z= 0.262 Chirality : 0.046 0.425 678 Planarity : 0.004 0.044 700 Dihedral : 3.549 18.853 583 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.13 % Allowed : 23.13 % Favored : 73.73 % 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: 1.59 (0.38), residues: 539 helix: 2.47 (0.30), residues: 325 sheet: None (None), residues: 0 loop : -1.29 (0.39), residues: 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 47 time to evaluate : 0.497 Fit side-chains outliers start: 13 outliers final: 12 residues processed: 58 average time/residue: 1.0276 time to fit residues: 62.4351 Evaluate side-chains 59 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 47 time to evaluate : 0.450 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 1 average time/residue: 0.1068 time to fit residues: 0.9368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 chunk 26 optimal weight: 0.9980 chunk 34 optimal weight: 20.0000 chunk 45 optimal weight: 0.0170 chunk 13 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 overall best weight: 0.4618 ------------------------------------------------------------------------------- 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: 0.7820 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4258 Z= 0.159 Angle : 0.521 9.174 5782 Z= 0.264 Chirality : 0.046 0.422 678 Planarity : 0.004 0.045 700 Dihedral : 3.556 19.146 583 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.13 % Allowed : 23.61 % Favored : 73.25 % 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: 1.64 (0.38), residues: 539 helix: 2.48 (0.30), residues: 325 sheet: None (None), residues: 0 loop : -1.22 (0.40), residues: 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 47 time to evaluate : 0.572 Fit side-chains outliers start: 13 outliers final: 12 residues processed: 58 average time/residue: 0.9910 time to fit residues: 60.3864 Evaluate side-chains 59 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 47 time to evaluate : 0.472 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 1 average time/residue: 0.0872 time to fit residues: 0.7558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 49 optimal weight: 0.0870 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.149592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.111168 restraints weight = 4979.614| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.36 r_work: 0.3134 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4258 Z= 0.196 Angle : 0.539 9.287 5782 Z= 0.274 Chirality : 0.046 0.418 678 Planarity : 0.004 0.044 700 Dihedral : 3.640 18.628 583 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.13 % Allowed : 23.86 % Favored : 73.01 % 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: 1.47 (0.38), residues: 539 helix: 2.12 (0.30), residues: 337 sheet: None (None), residues: 0 loop : -1.07 (0.41), residues: 202 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1865.07 seconds wall clock time: 33 minutes 47.39 seconds (2027.39 seconds total)