Starting phenix.real_space_refine on Fri Feb 16 19:54:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irp_35682/02_2024/8irp_35682_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irp_35682/02_2024/8irp_35682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irp_35682/02_2024/8irp_35682.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irp_35682/02_2024/8irp_35682.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irp_35682/02_2024/8irp_35682_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irp_35682/02_2024/8irp_35682_trim_updated.pdb" } resolution = 2.8 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 52 5.16 5 C 5300 2.51 5 N 1316 2.21 5 O 1474 1.98 5 H 8208 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16350 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 8130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 8130 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 516} Chain: "A" Number of atoms: 8130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 8130 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 516} Chain: "C" 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: "D" 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: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'H35': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'H35': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 8.05, per 1000 atoms: 0.49 Number of scatterers: 16350 At special positions: 0 Unit cell: (94.461, 109.779, 101.269, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 O 1474 8.00 N 1316 7.00 C 5300 6.00 H 8208 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 78 " - pdb=" SG CYS B 123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 83 " - pdb=" SG CYS B 111 " distance=2.03 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 254 " - pdb=" SG CYS B 287 " distance=2.03 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 123 " distance=2.03 Simple disulfide: pdb=" SG CYS A 83 " - pdb=" SG CYS A 111 " distance=2.03 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 254 " - pdb=" SG CYS A 287 " 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 C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG C 1 " - " ASN A 270 " " NAG D 1 " - " ASN B 270 " Time building additional restraints: 13.64 Conformation dependent library (CDL) restraints added in 1.8 seconds 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1940 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 2 sheets defined 60.6% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.84 Creating SS restraints... Processing helix chain 'B' and resid 20 through 29 Processing helix chain 'B' and resid 32 through 36 Processing helix chain 'B' and resid 39 through 42 No H-bonds generated for 'chain 'B' and resid 39 through 42' Processing helix chain 'B' and resid 47 through 74 removed outlier: 5.111A pdb=" N TYR B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE B 63 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LEU B 64 " --> pdb=" O MET B 60 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ALA B 65 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER B 74 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing helix chain 'B' and resid 109 through 112 Processing helix chain 'B' and resid 118 through 149 Processing helix chain 'B' and resid 160 through 168 removed outlier: 3.855A pdb=" N ALA B 164 " --> pdb=" O MET B 160 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR B 165 " --> pdb=" O GLY B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 200 Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'B' and resid 213 through 232 removed outlier: 4.331A pdb=" N SER B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 258 No H-bonds generated for 'chain 'B' and resid 256 through 258' Processing helix chain 'B' and resid 295 through 312 Processing helix chain 'B' and resid 318 through 331 Processing helix chain 'B' and resid 344 through 354 Processing helix chain 'B' and resid 377 through 405 Processing helix chain 'B' and resid 417 through 434 Processing helix chain 'B' and resid 443 through 450 Processing helix chain 'B' and resid 457 through 469 Processing helix chain 'B' and resid 473 through 476 No H-bonds generated for 'chain 'B' and resid 473 through 476' Processing helix chain 'B' and resid 481 through 501 Proline residue: B 486 - end of helix removed outlier: 3.547A pdb=" N MET B 496 " --> pdb=" O GLY B 492 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LYS B 497 " --> pdb=" O VAL B 493 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N SER B 498 " --> pdb=" O MET B 494 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N VAL B 499 " --> pdb=" O MET B 495 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N THR B 500 " --> pdb=" O MET B 496 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLU B 501 " --> pdb=" O LYS B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 522 Proline residue: B 512 - end of helix removed outlier: 3.834A pdb=" N MET B 520 " --> pdb=" O THR B 516 " (cutoff:3.500A) Proline residue: B 521 - end of helix Processing helix chain 'B' and resid 526 through 540 Processing helix chain 'B' and resid 542 through 553 Processing helix chain 'A' and resid 20 through 29 Processing helix chain 'A' and resid 32 through 36 Processing helix chain 'A' and resid 39 through 42 No H-bonds generated for 'chain 'A' and resid 39 through 42' Processing helix chain 'A' and resid 47 through 74 removed outlier: 5.112A pdb=" N TYR A 62 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE A 63 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LEU A 64 " --> pdb=" O MET A 60 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA A 65 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER A 74 " --> pdb=" O ILE A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 82 No H-bonds generated for 'chain 'A' and resid 80 through 82' Processing helix chain 'A' and resid 94 through 96 No H-bonds generated for 'chain 'A' and resid 94 through 96' Processing helix chain 'A' and resid 109 through 112 Processing helix chain 'A' and resid 118 through 149 Processing helix chain 'A' and resid 160 through 168 removed outlier: 3.855A pdb=" N ALA A 164 " --> pdb=" O MET A 160 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TYR A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 200 Processing helix chain 'A' and resid 204 through 210 Processing helix chain 'A' and resid 213 through 232 removed outlier: 4.332A pdb=" N SER A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 258 No H-bonds generated for 'chain 'A' and resid 256 through 258' Processing helix chain 'A' and resid 295 through 312 Processing helix chain 'A' and resid 318 through 331 Processing helix chain 'A' and resid 344 through 354 Processing helix chain 'A' and resid 377 through 405 Processing helix chain 'A' and resid 417 through 434 Processing helix chain 'A' and resid 443 through 450 Processing helix chain 'A' and resid 457 through 469 Processing helix chain 'A' and resid 473 through 476 No H-bonds generated for 'chain 'A' and resid 473 through 476' Processing helix chain 'A' and resid 481 through 501 Proline residue: A 486 - end of helix removed outlier: 3.546A pdb=" N MET A 496 " --> pdb=" O GLY A 492 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LYS A 497 " --> pdb=" O VAL A 493 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N SER A 498 " --> pdb=" O MET A 494 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N VAL A 499 " --> pdb=" O MET A 495 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N THR A 500 " --> pdb=" O MET A 496 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLU A 501 " --> pdb=" O LYS A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 522 Proline residue: A 512 - end of helix removed outlier: 3.833A pdb=" N MET A 520 " --> pdb=" O THR A 516 " (cutoff:3.500A) Proline residue: A 521 - end of helix Processing helix chain 'A' and resid 526 through 540 Processing helix chain 'A' and resid 542 through 553 Processing sheet with id= A, first strand: chain 'B' and resid 156 through 158 Processing sheet with id= B, first strand: chain 'A' and resid 156 through 158 418 hydrogen bonds defined for protein. 1218 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: 5.69 Time building geometry restraints manager: 14.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8204 1.03 - 1.23: 14 1.23 - 1.42: 3412 1.42 - 1.62: 4824 1.62 - 1.81: 84 Bond restraints: 16538 Sorted by residual: bond pdb=" C6 H35 A 701 " pdb=" N6 H35 A 701 " ideal model delta sigma weight residual 1.345 1.447 -0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" C6 H35 B 701 " pdb=" N6 H35 B 701 " ideal model delta sigma weight residual 1.345 1.447 -0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.465 -0.059 2.00e-02 2.50e+03 8.73e+00 bond pdb=" CAM H35 B 701 " pdb=" CAO H35 B 701 " ideal model delta sigma weight residual 1.429 1.386 0.043 2.00e-02 2.50e+03 4.67e+00 bond pdb=" CAM H35 A 701 " pdb=" CAO H35 A 701 " ideal model delta sigma weight residual 1.429 1.386 0.043 2.00e-02 2.50e+03 4.57e+00 ... (remaining 16533 not shown) Histogram of bond angle deviations from ideal: 99.42 - 106.79: 280 106.79 - 114.16: 20186 114.16 - 121.54: 6529 121.54 - 128.91: 2875 128.91 - 136.28: 56 Bond angle restraints: 29926 Sorted by residual: angle pdb=" N LEU B 248 " pdb=" CA LEU B 248 " pdb=" CB LEU B 248 " ideal model delta sigma weight residual 114.17 110.08 4.09 1.14e+00 7.69e-01 1.29e+01 angle pdb=" N LEU A 248 " pdb=" CA LEU A 248 " pdb=" CB LEU A 248 " ideal model delta sigma weight residual 114.17 110.09 4.08 1.14e+00 7.69e-01 1.28e+01 angle pdb=" C2 H35 A 701 " pdb=" N3 H35 A 701 " pdb=" C4 H35 A 701 " ideal model delta sigma weight residual 113.07 122.12 -9.05 3.00e+00 1.11e-01 9.11e+00 angle pdb=" C2 H35 B 701 " pdb=" N3 H35 B 701 " pdb=" C4 H35 B 701 " ideal model delta sigma weight residual 113.07 122.11 -9.04 3.00e+00 1.11e-01 9.07e+00 angle pdb=" CAP H35 A 701 " pdb=" CAK H35 A 701 " pdb=" OAL H35 A 701 " ideal model delta sigma weight residual 118.02 126.33 -8.31 3.00e+00 1.11e-01 7.67e+00 ... (remaining 29921 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.96: 7461 24.96 - 49.93: 296 49.93 - 74.89: 117 74.89 - 99.86: 4 99.86 - 124.82: 2 Dihedral angle restraints: 7880 sinusoidal: 4246 harmonic: 3634 Sorted by residual: dihedral pdb=" CA VAL A 484 " pdb=" C VAL A 484 " pdb=" N GLY A 485 " pdb=" CA GLY A 485 " ideal model delta harmonic sigma weight residual 180.00 143.50 36.50 0 5.00e+00 4.00e-02 5.33e+01 dihedral pdb=" CA VAL B 484 " pdb=" C VAL B 484 " pdb=" N GLY B 485 " pdb=" CA GLY B 485 " ideal model delta harmonic sigma weight residual 180.00 143.56 36.44 0 5.00e+00 4.00e-02 5.31e+01 dihedral pdb=" CA PHE B 332 " pdb=" C PHE B 332 " pdb=" N ARG B 333 " pdb=" CA ARG B 333 " ideal model delta harmonic sigma weight residual 180.00 -159.40 -20.60 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 7877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1324 0.099 - 0.199: 31 0.199 - 0.298: 0 0.298 - 0.398: 0 0.398 - 0.497: 1 Chirality restraints: 1356 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN B 270 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.18e+00 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 270 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-01 2.50e+01 7.93e-01 chirality pdb=" CA ILE A 266 " pdb=" N ILE A 266 " pdb=" C ILE A 266 " pdb=" CB ILE A 266 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01 ... (remaining 1353 not shown) Planarity restraints: 2434 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 270 " -0.094 2.00e-02 2.50e+03 7.85e-02 9.25e+01 pdb=" CG ASN B 270 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN B 270 " 0.044 2.00e-02 2.50e+03 pdb=" ND2 ASN B 270 " 0.085 2.00e-02 2.50e+03 pdb="HD21 ASN B 270 " 0.065 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " -0.120 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 486 " -0.039 5.00e-02 4.00e+02 5.81e-02 5.40e+00 pdb=" N PRO B 487 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO B 487 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 487 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 486 " -0.038 5.00e-02 4.00e+02 5.80e-02 5.38e+00 pdb=" N PRO A 487 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 487 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 487 " -0.033 5.00e-02 4.00e+02 ... (remaining 2431 not shown) Histogram of nonbonded interaction distances: 1.32 - 1.98: 140 1.98 - 2.63: 21658 2.63 - 3.29: 52641 3.29 - 3.94: 67382 3.94 - 4.60: 105709 Nonbonded interactions: 247530 Sorted by model distance: nonbonded pdb="HG23 THR A 162 " pdb=" HE1 PHE A 386 " model vdw 1.324 2.270 nonbonded pdb="HG21 THR A 162 " pdb=" HD2 PRO A 438 " model vdw 1.376 2.440 nonbonded pdb=" OD1 ASP A 130 " pdb=" HE2 HIS A 360 " model vdw 1.603 1.850 nonbonded pdb=" OD1 ASP B 130 " pdb=" HE2 HIS B 360 " model vdw 1.603 1.850 nonbonded pdb="HH22 ARG B 333 " pdb=" OD1 ASP B 347 " model vdw 1.606 1.850 ... (remaining 247525 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 0.570 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: 0.260 Extract box with map and model: 3.860 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 54.740 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 73.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 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 : 0.004 0.102 8330 Z= 0.239 Angle : 0.612 9.054 11338 Z= 0.310 Chirality : 0.042 0.497 1356 Planarity : 0.004 0.058 1400 Dihedral : 13.359 124.823 2936 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.19 (0.26), residues: 1076 helix: 1.78 (0.20), residues: 654 sheet: -5.81 (0.22), residues: 20 loop : -0.48 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 482 HIS 0.001 0.000 HIS A 541 PHE 0.022 0.001 PHE A 203 TYR 0.010 0.001 TYR B 524 ARG 0.002 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.135 Fit side-chains outliers start: 0 outliers final: 2 residues processed: 91 average time/residue: 2.2451 time to fit residues: 219.7629 Evaluate side-chains 80 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain A residue 266 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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: 0.8500 moved from start: 0.0658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8330 Z= 0.337 Angle : 0.562 8.044 11338 Z= 0.292 Chirality : 0.042 0.151 1356 Planarity : 0.004 0.058 1400 Dihedral : 8.003 106.425 1238 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.18 % Favored : 95.63 % Rotamer: Outliers : 1.05 % Allowed : 4.43 % Favored : 94.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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 (0.26), residues: 1076 helix: 1.55 (0.20), residues: 652 sheet: -5.65 (0.28), residues: 20 loop : -0.45 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 380 HIS 0.002 0.001 HIS B 350 PHE 0.014 0.002 PHE A 166 TYR 0.011 0.002 TYR B 388 ARG 0.003 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 1.340 Fit side-chains REVERT: B 494 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.7077 (mpp) REVERT: A 494 MET cc_start: 0.7715 (OUTLIER) cc_final: 0.7055 (mpp) REVERT: A 509 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7362 (mt-10) outliers start: 9 outliers final: 3 residues processed: 81 average time/residue: 2.3439 time to fit residues: 204.1013 Evaluate side-chains 82 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 77 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 544 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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: 0.8478 moved from start: 0.0663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8330 Z= 0.200 Angle : 0.514 9.278 11338 Z= 0.266 Chirality : 0.040 0.155 1356 Planarity : 0.004 0.058 1400 Dihedral : 7.366 95.834 1234 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.93 % Allowed : 6.41 % Favored : 92.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.04 (0.26), residues: 1076 helix: 1.66 (0.20), residues: 654 sheet: -5.64 (0.31), residues: 20 loop : -0.54 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 380 HIS 0.001 0.000 HIS A 541 PHE 0.012 0.001 PHE A 414 TYR 0.010 0.001 TYR B 388 ARG 0.001 0.000 ARG A 259 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 78 time to evaluate : 1.373 Fit side-chains REVERT: B 494 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7063 (mpp) REVERT: A 494 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.7021 (mpp) REVERT: A 509 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7340 (mt-10) outliers start: 8 outliers final: 4 residues processed: 82 average time/residue: 2.3208 time to fit residues: 204.5611 Evaluate side-chains 82 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 76 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 544 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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: 0.8475 moved from start: 0.0762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8330 Z= 0.205 Angle : 0.515 10.813 11338 Z= 0.263 Chirality : 0.039 0.127 1356 Planarity : 0.004 0.059 1400 Dihedral : 6.585 78.996 1234 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.17 % Allowed : 6.76 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.11 (0.26), residues: 1076 helix: 1.73 (0.20), residues: 654 sheet: -5.53 (0.34), residues: 20 loop : -0.56 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 380 HIS 0.002 0.000 HIS B 541 PHE 0.015 0.001 PHE A 203 TYR 0.009 0.001 TYR A 388 ARG 0.003 0.000 ARG A 23 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 78 time to evaluate : 1.272 Fit side-chains REVERT: B 494 MET cc_start: 0.7691 (OUTLIER) cc_final: 0.7017 (mpp) REVERT: B 496 MET cc_start: 0.8709 (tpp) cc_final: 0.8237 (tpt) REVERT: A 494 MET cc_start: 0.7641 (OUTLIER) cc_final: 0.7007 (mpp) REVERT: A 509 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7352 (mt-10) outliers start: 10 outliers final: 4 residues processed: 82 average time/residue: 2.3483 time to fit residues: 206.8131 Evaluate side-chains 82 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 76 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 544 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 53 optimal weight: 0.0770 chunk 93 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- 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: 0.8517 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8330 Z= 0.331 Angle : 0.572 9.906 11338 Z= 0.298 Chirality : 0.042 0.129 1356 Planarity : 0.004 0.058 1400 Dihedral : 5.607 47.582 1234 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.81 % Favored : 96.00 % Rotamer: Outliers : 0.93 % Allowed : 7.81 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.79 (0.26), residues: 1076 helix: 1.45 (0.20), residues: 644 sheet: -5.28 (0.42), residues: 20 loop : -0.61 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 380 HIS 0.003 0.001 HIS B 350 PHE 0.015 0.002 PHE A 189 TYR 0.011 0.002 TYR B 388 ARG 0.003 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 1.340 Fit side-chains REVERT: B 494 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.7071 (mpp) REVERT: A 494 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.7050 (mpp) REVERT: A 509 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7343 (mt-10) outliers start: 8 outliers final: 2 residues processed: 77 average time/residue: 2.4969 time to fit residues: 205.8055 Evaluate side-chains 76 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 544 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 34 optimal weight: 0.0370 chunk 54 optimal weight: 4.9990 overall best weight: 1.0062 ------------------------------------------------------------------------------- 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: 0.8475 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8330 Z= 0.172 Angle : 0.492 5.892 11338 Z= 0.256 Chirality : 0.039 0.125 1356 Planarity : 0.004 0.061 1400 Dihedral : 4.966 47.186 1234 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.70 % Allowed : 8.86 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.06 (0.26), residues: 1076 helix: 1.73 (0.20), residues: 648 sheet: -5.43 (0.38), residues: 20 loop : -0.62 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 380 HIS 0.001 0.000 HIS B 541 PHE 0.011 0.001 PHE A 414 TYR 0.009 0.001 TYR A 388 ARG 0.003 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 1.333 Fit side-chains REVERT: B 494 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7013 (mpp) REVERT: A 494 MET cc_start: 0.7660 (OUTLIER) cc_final: 0.7009 (mpp) REVERT: A 509 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7372 (mt-10) outliers start: 6 outliers final: 3 residues processed: 81 average time/residue: 2.2504 time to fit residues: 196.5432 Evaluate side-chains 82 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 77 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 544 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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: 0.8495 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8330 Z= 0.241 Angle : 0.511 5.365 11338 Z= 0.268 Chirality : 0.040 0.127 1356 Planarity : 0.004 0.060 1400 Dihedral : 4.958 45.612 1234 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.93 % Allowed : 9.09 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.01 (0.26), residues: 1076 helix: 1.68 (0.20), residues: 648 sheet: -5.36 (0.38), residues: 20 loop : -0.62 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 380 HIS 0.002 0.001 HIS A 541 PHE 0.016 0.002 PHE A 203 TYR 0.009 0.001 TYR B 388 ARG 0.004 0.000 ARG A 23 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 74 time to evaluate : 1.242 Fit side-chains REVERT: B 494 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.7033 (mpp) REVERT: A 494 MET cc_start: 0.7682 (OUTLIER) cc_final: 0.7013 (mpp) REVERT: A 509 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7345 (mt-10) outliers start: 8 outliers final: 4 residues processed: 78 average time/residue: 2.4570 time to fit residues: 205.6107 Evaluate side-chains 80 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 74 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 544 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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: 0.8483 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8330 Z= 0.198 Angle : 0.496 5.181 11338 Z= 0.259 Chirality : 0.039 0.125 1356 Planarity : 0.004 0.060 1400 Dihedral : 4.877 45.047 1234 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.70 % Allowed : 9.56 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.14 (0.26), residues: 1076 helix: 1.79 (0.20), residues: 646 sheet: -5.42 (0.38), residues: 20 loop : -0.56 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 380 HIS 0.001 0.000 HIS B 541 PHE 0.015 0.001 PHE A 203 TYR 0.009 0.001 TYR A 388 ARG 0.005 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 74 time to evaluate : 1.245 Fit side-chains REVERT: B 494 MET cc_start: 0.7692 (OUTLIER) cc_final: 0.7018 (mpp) REVERT: A 494 MET cc_start: 0.7671 (OUTLIER) cc_final: 0.7009 (mpp) REVERT: A 509 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7342 (mt-10) outliers start: 6 outliers final: 4 residues processed: 78 average time/residue: 2.4493 time to fit residues: 204.8908 Evaluate side-chains 82 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 76 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 544 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.8464 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8330 Z= 0.155 Angle : 0.479 4.984 11338 Z= 0.250 Chirality : 0.038 0.123 1356 Planarity : 0.004 0.061 1400 Dihedral : 4.722 44.660 1234 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.47 % Allowed : 10.37 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.30 (0.26), residues: 1076 helix: 1.92 (0.21), residues: 646 sheet: -5.47 (0.34), residues: 20 loop : -0.49 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 482 HIS 0.001 0.000 HIS B 541 PHE 0.015 0.001 PHE B 203 TYR 0.008 0.001 TYR B 388 ARG 0.006 0.000 ARG A 23 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 79 time to evaluate : 1.324 Fit side-chains REVERT: B 494 MET cc_start: 0.7660 (OUTLIER) cc_final: 0.7000 (mpp) REVERT: A 494 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.6984 (mpp) REVERT: A 509 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7341 (mt-10) outliers start: 4 outliers final: 2 residues processed: 81 average time/residue: 2.3412 time to fit residues: 203.8369 Evaluate side-chains 82 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 494 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 48 optimal weight: 0.4980 chunk 71 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 8 optimal weight: 0.0170 chunk 66 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.8820 ------------------------------------------------------------------------------- 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: 0.8462 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8330 Z= 0.162 Angle : 0.480 5.036 11338 Z= 0.250 Chirality : 0.038 0.124 1356 Planarity : 0.004 0.061 1400 Dihedral : 4.664 45.361 1234 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.58 % Allowed : 10.61 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.35 (0.26), residues: 1076 helix: 1.90 (0.20), residues: 652 sheet: -5.51 (0.33), residues: 20 loop : -0.38 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 482 HIS 0.001 0.000 HIS A 541 PHE 0.015 0.001 PHE B 203 TYR 0.008 0.001 TYR B 388 ARG 0.005 0.000 ARG B 23 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 78 time to evaluate : 1.227 Fit side-chains REVERT: B 494 MET cc_start: 0.7675 (OUTLIER) cc_final: 0.7026 (mpp) REVERT: A 494 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.6999 (mpp) REVERT: A 509 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7341 (mt-10) outliers start: 5 outliers final: 2 residues processed: 81 average time/residue: 2.4075 time to fit residues: 211.3329 Evaluate side-chains 81 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 77 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 494 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 88 optimal weight: 0.0010 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.1992 ------------------------------------------------------------------------------- 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 = 0.3238 r_free = 0.3238 target = 0.111761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.089752 restraints weight = 29538.674| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.66 r_work: 0.2850 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8330 Z= 0.187 Angle : 0.488 5.176 11338 Z= 0.254 Chirality : 0.039 0.123 1356 Planarity : 0.004 0.060 1400 Dihedral : 4.680 45.368 1234 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.58 % Allowed : 10.61 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.32 (0.26), residues: 1076 helix: 1.88 (0.20), residues: 652 sheet: -5.49 (0.33), residues: 20 loop : -0.40 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 482 HIS 0.001 0.000 HIS B 541 PHE 0.016 0.001 PHE B 203 TYR 0.008 0.001 TYR B 388 ARG 0.004 0.000 ARG B 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5101.59 seconds wall clock time: 90 minutes 35.05 seconds (5435.05 seconds total)