Starting phenix.real_space_refine on Sat Apr 6 13:19:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j74_36025/04_2024/8j74_36025.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j74_36025/04_2024/8j74_36025.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j74_36025/04_2024/8j74_36025.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j74_36025/04_2024/8j74_36025.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j74_36025/04_2024/8j74_36025.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j74_36025/04_2024/8j74_36025.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.061 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 5546 2.51 5 N 1214 2.21 5 O 1488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 315": "OE1" <-> "OE2" Residue "A TYR 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 315": "OE1" <-> "OE2" Residue "B TYR 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8288 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 3959 Classifications: {'peptide': 515} Link IDs: {'PTRANS': 22, 'TRANS': 492} Chain: "B" Number of atoms: 3959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 3959 Classifications: {'peptide': 515} Link IDs: {'PTRANS': 22, 'TRANS': 492} Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 146 Unusual residues: {'AV0': 1, 'HC6': 1, 'R16': 1, 'Y01': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 146 Unusual residues: {'AV0': 1, 'HC6': 1, 'R16': 1, 'Y01': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 5.09, per 1000 atoms: 0.61 Number of scatterers: 8288 At special positions: 0 Unit cell: (100.86, 100.86, 95.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1488 8.00 N 1214 7.00 C 5546 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG E 1 " - " ASN A 301 " " NAG F 1 " - " ASN B 301 " Time building additional restraints: 3.44 Conformation dependent library (CDL) restraints added in 1.5 seconds 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1872 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 2 sheets defined 77.5% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 4 through 29 removed outlier: 3.548A pdb=" N LEU A 8 " --> pdb=" O HIS A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 45 Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 50 through 63 removed outlier: 3.529A pdb=" N VAL A 63 " --> pdb=" O THR A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 77 removed outlier: 3.815A pdb=" N THR A 71 " --> pdb=" O TYR A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 102 Processing helix chain 'A' and resid 103 through 109 removed outlier: 3.645A pdb=" N ARG A 107 " --> pdb=" O ALA A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 122 removed outlier: 4.309A pdb=" N PHE A 118 " --> pdb=" O MET A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 130 Processing helix chain 'A' and resid 130 through 157 removed outlier: 4.235A pdb=" N ALA A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 179 removed outlier: 3.721A pdb=" N VAL A 178 " --> pdb=" O LEU A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 200 removed outlier: 3.714A pdb=" N VAL A 190 " --> pdb=" O TYR A 186 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE A 193 " --> pdb=" O VAL A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 208 Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 236 through 250 Processing helix chain 'A' and resid 254 through 262 Processing helix chain 'A' and resid 266 through 297 removed outlier: 4.168A pdb=" N ALA A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) Proline residue: A 287 - end of helix Processing helix chain 'A' and resid 309 through 314 Processing helix chain 'A' and resid 315 through 318 Processing helix chain 'A' and resid 319 through 327 removed outlier: 3.677A pdb=" N GLN A 325 " --> pdb=" O PRO A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 363 removed outlier: 3.871A pdb=" N PHE A 335 " --> pdb=" O TYR A 331 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 399 removed outlier: 3.561A pdb=" N PHE A 386 " --> pdb=" O ARG A 382 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR A 399 " --> pdb=" O MET A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 426 Proline residue: A 419 - end of helix Processing helix chain 'A' and resid 431 through 448 removed outlier: 3.852A pdb=" N ALA A 437 " --> pdb=" O TYR A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 505 removed outlier: 4.106A pdb=" N MET A 484 " --> pdb=" O LYS A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 512 removed outlier: 3.725A pdb=" N LEU A 511 " --> pdb=" O PRO A 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 29 removed outlier: 3.548A pdb=" N LEU B 8 " --> pdb=" O HIS B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 45 Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 50 through 63 removed outlier: 3.529A pdb=" N VAL B 63 " --> pdb=" O THR B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 77 removed outlier: 3.815A pdb=" N THR B 71 " --> pdb=" O TYR B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 102 Processing helix chain 'B' and resid 103 through 109 removed outlier: 3.645A pdb=" N ARG B 107 " --> pdb=" O ALA B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 122 removed outlier: 4.309A pdb=" N PHE B 118 " --> pdb=" O MET B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 130 Processing helix chain 'B' and resid 130 through 157 removed outlier: 4.235A pdb=" N ALA B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 179 removed outlier: 3.721A pdb=" N VAL B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 200 removed outlier: 3.714A pdb=" N VAL B 190 " --> pdb=" O TYR B 186 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE B 193 " --> pdb=" O VAL B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 208 Processing helix chain 'B' and resid 233 through 235 No H-bonds generated for 'chain 'B' and resid 233 through 235' Processing helix chain 'B' and resid 236 through 250 Processing helix chain 'B' and resid 254 through 262 Processing helix chain 'B' and resid 266 through 297 removed outlier: 4.168A pdb=" N ALA B 270 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE B 275 " --> pdb=" O GLN B 271 " (cutoff:3.500A) Proline residue: B 287 - end of helix Processing helix chain 'B' and resid 309 through 314 Processing helix chain 'B' and resid 315 through 318 Processing helix chain 'B' and resid 319 through 327 removed outlier: 3.677A pdb=" N GLN B 325 " --> pdb=" O PRO B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 363 removed outlier: 3.871A pdb=" N PHE B 335 " --> pdb=" O TYR B 331 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG B 361 " --> pdb=" O SER B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 399 removed outlier: 3.561A pdb=" N PHE B 386 " --> pdb=" O ARG B 382 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR B 399 " --> pdb=" O MET B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 426 Proline residue: B 419 - end of helix Processing helix chain 'B' and resid 431 through 448 removed outlier: 3.852A pdb=" N ALA B 437 " --> pdb=" O TYR B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 505 removed outlier: 4.106A pdb=" N MET B 484 " --> pdb=" O LYS B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 512 removed outlier: 3.725A pdb=" N LEU B 511 " --> pdb=" O PRO B 508 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 466 through 467 Processing sheet with id=AA2, first strand: chain 'B' and resid 466 through 467 552 hydrogen bonds defined for protein. 1638 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: 2.35 Time building geometry restraints manager: 3.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1255 1.32 - 1.45: 2473 1.45 - 1.57: 4730 1.57 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 8528 Sorted by residual: bond pdb=" CB ASP B 411 " pdb=" CG ASP B 411 " ideal model delta sigma weight residual 1.516 1.447 0.069 2.50e-02 1.60e+03 7.58e+00 bond pdb=" CB ASP A 411 " pdb=" CG ASP A 411 " ideal model delta sigma weight residual 1.516 1.447 0.069 2.50e-02 1.60e+03 7.58e+00 bond pdb=" CA ASP B 411 " pdb=" C ASP B 411 " ideal model delta sigma weight residual 1.524 1.497 0.027 1.27e-02 6.20e+03 4.39e+00 bond pdb=" CA ASP A 411 " pdb=" C ASP A 411 " ideal model delta sigma weight residual 1.524 1.497 0.027 1.27e-02 6.20e+03 4.39e+00 bond pdb=" N PHE A 477 " pdb=" CA PHE A 477 " ideal model delta sigma weight residual 1.457 1.484 -0.028 1.41e-02 5.03e+03 3.83e+00 ... (remaining 8523 not shown) Histogram of bond angle deviations from ideal: 99.50 - 106.43: 244 106.43 - 113.35: 4720 113.35 - 120.28: 3186 120.28 - 127.21: 3410 127.21 - 134.13: 100 Bond angle restraints: 11660 Sorted by residual: angle pdb=" N LEU A 482 " pdb=" CA LEU A 482 " pdb=" C LEU A 482 " ideal model delta sigma weight residual 111.28 105.66 5.62 1.09e+00 8.42e-01 2.65e+01 angle pdb=" N LEU B 482 " pdb=" CA LEU B 482 " pdb=" C LEU B 482 " ideal model delta sigma weight residual 111.28 105.67 5.61 1.09e+00 8.42e-01 2.65e+01 angle pdb=" N TYR A 364 " pdb=" CA TYR A 364 " pdb=" C TYR A 364 " ideal model delta sigma weight residual 112.04 118.40 -6.36 1.44e+00 4.82e-01 1.95e+01 angle pdb=" N TYR B 364 " pdb=" CA TYR B 364 " pdb=" C TYR B 364 " ideal model delta sigma weight residual 112.04 118.40 -6.36 1.44e+00 4.82e-01 1.95e+01 angle pdb=" N ILE B 332 " pdb=" CA ILE B 332 " pdb=" C ILE B 332 " ideal model delta sigma weight residual 111.81 108.01 3.80 8.60e-01 1.35e+00 1.95e+01 ... (remaining 11655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.42: 4774 26.42 - 52.84: 300 52.84 - 79.26: 60 79.26 - 105.68: 72 105.68 - 132.10: 32 Dihedral angle restraints: 5238 sinusoidal: 2276 harmonic: 2962 Sorted by residual: dihedral pdb=" CCF AV0 B 601 " pdb=" CCQ AV0 B 601 " pdb=" OCB AV0 B 601 " pdb=" CCS AV0 B 601 " ideal model delta sinusoidal sigma weight residual -112.55 19.55 -132.10 1 3.00e+01 1.11e-03 1.78e+01 dihedral pdb=" CCF AV0 A 702 " pdb=" CCQ AV0 A 702 " pdb=" OCB AV0 A 702 " pdb=" CCS AV0 A 702 " ideal model delta sinusoidal sigma weight residual -112.55 19.55 -132.10 1 3.00e+01 1.11e-03 1.78e+01 dihedral pdb=" CCH AV0 B 601 " pdb=" CCQ AV0 B 601 " pdb=" OCB AV0 B 601 " pdb=" CCS AV0 B 601 " ideal model delta sinusoidal sigma weight residual 127.39 -100.76 -131.85 1 3.00e+01 1.11e-03 1.78e+01 ... (remaining 5235 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1105 0.055 - 0.110: 227 0.110 - 0.164: 28 0.164 - 0.219: 14 0.219 - 0.274: 2 Chirality restraints: 1376 Sorted by residual: chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CB ILE A 252 " pdb=" CA ILE A 252 " pdb=" CG1 ILE A 252 " pdb=" CG2 ILE A 252 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1373 not shown) Planarity restraints: 1372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 455 " -0.007 2.00e-02 2.50e+03 1.30e-02 3.40e+00 pdb=" CG TYR B 455 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR B 455 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 455 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR B 455 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 455 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 455 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 455 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 455 " -0.007 2.00e-02 2.50e+03 1.30e-02 3.40e+00 pdb=" CG TYR A 455 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 455 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR A 455 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR A 455 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 455 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 455 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 455 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 455 " -0.008 2.00e-02 2.50e+03 1.58e-02 2.50e+00 pdb=" C TYR A 455 " 0.027 2.00e-02 2.50e+03 pdb=" O TYR A 455 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU A 456 " -0.009 2.00e-02 2.50e+03 ... (remaining 1369 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 887 2.74 - 3.28: 8846 3.28 - 3.82: 14360 3.82 - 4.36: 15495 4.36 - 4.90: 27129 Nonbonded interactions: 66717 Sorted by model distance: nonbonded pdb=" OG SER B 34 " pdb=" OE1 GLU B 37 " model vdw 2.203 2.440 nonbonded pdb=" OG SER A 34 " pdb=" OE1 GLU A 37 " model vdw 2.204 2.440 nonbonded pdb=" OG SER A 34 " pdb=" OE1 GLU A 36 " model vdw 2.232 2.440 nonbonded pdb=" OG SER B 34 " pdb=" OE1 GLU B 36 " model vdw 2.232 2.440 nonbonded pdb=" O PHE A 444 " pdb=" OG1 THR A 448 " model vdw 2.281 2.440 ... (remaining 66712 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 517 or resid 704)) selection = (chain 'B' and (resid 3 through 517 or resid 604)) } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.020 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 26.070 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 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 0.069 8528 Z= 0.258 Angle : 0.734 8.405 11660 Z= 0.363 Chirality : 0.047 0.274 1376 Planarity : 0.004 0.037 1370 Dihedral : 24.907 132.103 3366 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.00 % Allowed : 25.30 % Favored : 74.70 % 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: 0.74 (0.29), residues: 1026 helix: 1.49 (0.21), residues: 734 sheet: None (None), residues: 0 loop : -2.18 (0.39), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 300 HIS 0.005 0.001 HIS B 221 PHE 0.012 0.001 PHE A 118 TYR 0.030 0.002 TYR A 455 ARG 0.009 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 0.974 Fit side-chains REVERT: A 130 LEU cc_start: 0.8802 (mp) cc_final: 0.8563 (mp) REVERT: A 455 TYR cc_start: 0.5322 (p90) cc_final: 0.5001 (p90) REVERT: B 130 LEU cc_start: 0.8787 (mp) cc_final: 0.8544 (mp) REVERT: B 455 TYR cc_start: 0.5323 (p90) cc_final: 0.5000 (p90) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.1812 time to fit residues: 40.7393 Evaluate side-chains 144 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 92 optimal weight: 0.1980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 ASN B 491 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8528 Z= 0.203 Angle : 0.736 10.071 11660 Z= 0.327 Chirality : 0.045 0.239 1376 Planarity : 0.004 0.029 1370 Dihedral : 20.257 146.458 1716 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.65 % Allowed : 23.37 % 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: 0.95 (0.29), residues: 1026 helix: 1.55 (0.20), residues: 740 sheet: None (None), residues: 0 loop : -1.88 (0.41), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 406 HIS 0.003 0.001 HIS B 221 PHE 0.009 0.001 PHE B 461 TYR 0.013 0.001 TYR A 414 ARG 0.004 0.001 ARG B 260 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 142 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8789 (mp) REVERT: A 318 MET cc_start: 0.7176 (ppp) cc_final: 0.6484 (ppp) REVERT: A 455 TYR cc_start: 0.5606 (p90) cc_final: 0.5346 (p90) REVERT: B 130 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8786 (mp) REVERT: B 318 MET cc_start: 0.7172 (ppp) cc_final: 0.6467 (ppp) REVERT: B 455 TYR cc_start: 0.5602 (p90) cc_final: 0.5343 (p90) outliers start: 22 outliers final: 12 residues processed: 160 average time/residue: 0.1841 time to fit residues: 43.0375 Evaluate side-chains 141 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 127 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 431 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 63 optimal weight: 0.0980 chunk 25 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 ASN B 491 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8528 Z= 0.196 Angle : 0.659 9.241 11660 Z= 0.304 Chirality : 0.042 0.236 1376 Planarity : 0.004 0.049 1370 Dihedral : 15.502 153.716 1716 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 5.66 % Allowed : 21.08 % 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: 0.96 (0.29), residues: 1026 helix: 1.55 (0.20), residues: 748 sheet: None (None), residues: 0 loop : -1.93 (0.42), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 300 HIS 0.002 0.000 HIS B 221 PHE 0.006 0.001 PHE B 140 TYR 0.016 0.001 TYR A 439 ARG 0.005 0.001 ARG A 260 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 148 time to evaluate : 0.933 Fit side-chains REVERT: A 62 TRP cc_start: 0.7750 (m100) cc_final: 0.7202 (m100) REVERT: A 260 ARG cc_start: 0.8442 (tpp80) cc_final: 0.8138 (tpp80) REVERT: A 318 MET cc_start: 0.7286 (ppp) cc_final: 0.6451 (ppp) REVERT: A 455 TYR cc_start: 0.5633 (p90) cc_final: 0.5340 (p90) REVERT: B 260 ARG cc_start: 0.8433 (tpp80) cc_final: 0.8220 (tpp80) REVERT: B 318 MET cc_start: 0.7291 (ppp) cc_final: 0.6440 (ppp) REVERT: B 455 TYR cc_start: 0.5648 (p90) cc_final: 0.5350 (p90) outliers start: 47 outliers final: 20 residues processed: 184 average time/residue: 0.1669 time to fit residues: 44.6985 Evaluate side-chains 153 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 133 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 431 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 GLN A 491 ASN B 365 GLN B 491 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8528 Z= 0.193 Angle : 0.643 9.355 11660 Z= 0.299 Chirality : 0.041 0.240 1376 Planarity : 0.003 0.025 1370 Dihedral : 14.599 157.275 1716 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 4.46 % Allowed : 22.41 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.29), residues: 1026 helix: 1.54 (0.20), residues: 748 sheet: None (None), residues: 0 loop : -1.88 (0.43), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 406 HIS 0.001 0.000 HIS A 209 PHE 0.005 0.001 PHE B 140 TYR 0.012 0.001 TYR A 439 ARG 0.005 0.000 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 145 time to evaluate : 0.949 Fit side-chains REVERT: A 62 TRP cc_start: 0.7703 (m100) cc_final: 0.7221 (m100) REVERT: A 260 ARG cc_start: 0.8537 (tpp80) cc_final: 0.7971 (tpp80) REVERT: A 318 MET cc_start: 0.7022 (ppp) cc_final: 0.5977 (ppp) REVERT: A 455 TYR cc_start: 0.5692 (p90) cc_final: 0.5404 (p90) REVERT: B 62 TRP cc_start: 0.7713 (m100) cc_final: 0.7230 (m100) REVERT: B 116 ASP cc_start: 0.7864 (OUTLIER) cc_final: 0.7611 (t0) REVERT: B 260 ARG cc_start: 0.8542 (tpp80) cc_final: 0.7976 (tpp80) REVERT: B 318 MET cc_start: 0.7023 (ppp) cc_final: 0.5964 (ppp) REVERT: B 455 TYR cc_start: 0.5677 (p90) cc_final: 0.5385 (p90) outliers start: 37 outliers final: 32 residues processed: 173 average time/residue: 0.1723 time to fit residues: 42.9619 Evaluate side-chains 164 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 131 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 431 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 50 optimal weight: 0.0970 chunk 88 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 33 optimal weight: 0.0980 chunk 19 optimal weight: 3.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 ASN B 491 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8528 Z= 0.170 Angle : 0.604 9.369 11660 Z= 0.286 Chirality : 0.041 0.239 1376 Planarity : 0.003 0.025 1370 Dihedral : 14.228 156.178 1716 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.34 % Allowed : 24.58 % Favored : 71.08 % 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: 1.01 (0.29), residues: 1026 helix: 1.58 (0.20), residues: 748 sheet: None (None), residues: 0 loop : -1.90 (0.42), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 300 HIS 0.000 0.000 HIS A 209 PHE 0.006 0.001 PHE A 131 TYR 0.014 0.001 TYR A 439 ARG 0.005 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 158 time to evaluate : 0.940 Fit side-chains REVERT: A 62 TRP cc_start: 0.7675 (m100) cc_final: 0.7298 (m100) REVERT: A 116 ASP cc_start: 0.7844 (OUTLIER) cc_final: 0.7579 (t0) REVERT: A 318 MET cc_start: 0.7120 (ppp) cc_final: 0.6775 (ppp) REVERT: A 455 TYR cc_start: 0.5687 (p90) cc_final: 0.5398 (p90) REVERT: A 484 MET cc_start: 0.8460 (ppp) cc_final: 0.8199 (ppp) REVERT: B 62 TRP cc_start: 0.7664 (m100) cc_final: 0.7297 (m100) REVERT: B 116 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7567 (t0) REVERT: B 318 MET cc_start: 0.7118 (ppp) cc_final: 0.6764 (ppp) REVERT: B 455 TYR cc_start: 0.5682 (p90) cc_final: 0.5398 (p90) REVERT: B 484 MET cc_start: 0.8452 (ppp) cc_final: 0.8194 (ppp) outliers start: 36 outliers final: 28 residues processed: 182 average time/residue: 0.1648 time to fit residues: 43.3812 Evaluate side-chains 171 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 141 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 431 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 0.4980 chunk 8 optimal weight: 0.8980 chunk 32 optimal weight: 0.0370 chunk 51 optimal weight: 10.0000 chunk 95 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 ASN B 491 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8528 Z= 0.174 Angle : 0.632 10.650 11660 Z= 0.297 Chirality : 0.041 0.239 1376 Planarity : 0.003 0.026 1370 Dihedral : 13.813 156.429 1716 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.82 % Allowed : 25.06 % Favored : 70.12 % 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: 1.01 (0.29), residues: 1026 helix: 1.60 (0.20), residues: 746 sheet: None (None), residues: 0 loop : -1.97 (0.42), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 300 HIS 0.001 0.000 HIS A 209 PHE 0.011 0.001 PHE B 140 TYR 0.013 0.001 TYR B 439 ARG 0.007 0.001 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 147 time to evaluate : 0.872 Fit side-chains REVERT: A 62 TRP cc_start: 0.7637 (m100) cc_final: 0.7322 (m100) REVERT: A 116 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7620 (t0) REVERT: A 182 TYR cc_start: 0.7985 (OUTLIER) cc_final: 0.7620 (m-10) REVERT: A 229 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8291 (mp) REVERT: A 318 MET cc_start: 0.7180 (ppp) cc_final: 0.6863 (ppp) REVERT: A 455 TYR cc_start: 0.5760 (p90) cc_final: 0.5458 (p90) REVERT: B 62 TRP cc_start: 0.7629 (m100) cc_final: 0.7329 (m100) REVERT: B 116 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7614 (t0) REVERT: B 182 TYR cc_start: 0.7991 (OUTLIER) cc_final: 0.7621 (m-10) REVERT: B 229 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8293 (mp) REVERT: B 318 MET cc_start: 0.7179 (ppp) cc_final: 0.6855 (ppp) REVERT: B 455 TYR cc_start: 0.5754 (p90) cc_final: 0.5456 (p90) outliers start: 40 outliers final: 28 residues processed: 174 average time/residue: 0.1511 time to fit residues: 39.2866 Evaluate side-chains 170 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 136 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 431 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 83 optimal weight: 0.0370 chunk 98 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 39 optimal weight: 0.0060 chunk 58 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 ASN B 491 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8528 Z= 0.171 Angle : 0.605 9.418 11660 Z= 0.289 Chirality : 0.041 0.240 1376 Planarity : 0.003 0.026 1370 Dihedral : 12.990 156.700 1716 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 4.94 % Allowed : 24.46 % Favored : 70.60 % 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: 1.05 (0.29), residues: 1026 helix: 1.63 (0.20), residues: 746 sheet: None (None), residues: 0 loop : -1.95 (0.42), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 300 HIS 0.001 0.000 HIS B 209 PHE 0.004 0.001 PHE A 140 TYR 0.015 0.001 TYR B 439 ARG 0.008 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 148 time to evaluate : 0.885 Fit side-chains REVERT: A 62 TRP cc_start: 0.7633 (m100) cc_final: 0.7358 (m100) REVERT: A 116 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7539 (t0) REVERT: A 182 TYR cc_start: 0.7999 (OUTLIER) cc_final: 0.7575 (m-10) REVERT: A 229 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8276 (mp) REVERT: A 318 MET cc_start: 0.7273 (ppp) cc_final: 0.6978 (ppp) REVERT: A 485 VAL cc_start: 0.8798 (p) cc_final: 0.8574 (p) REVERT: B 62 TRP cc_start: 0.7605 (m100) cc_final: 0.7351 (m100) REVERT: B 116 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7539 (t0) REVERT: B 182 TYR cc_start: 0.8002 (OUTLIER) cc_final: 0.7586 (m-10) REVERT: B 229 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8272 (mp) REVERT: B 318 MET cc_start: 0.7273 (ppp) cc_final: 0.6966 (ppp) REVERT: B 484 MET cc_start: 0.8527 (ppp) cc_final: 0.8204 (ppp) outliers start: 41 outliers final: 28 residues processed: 176 average time/residue: 0.1608 time to fit residues: 41.7558 Evaluate side-chains 179 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 145 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 431 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 ASN B 491 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8528 Z= 0.187 Angle : 0.643 12.028 11660 Z= 0.301 Chirality : 0.041 0.240 1376 Planarity : 0.003 0.028 1370 Dihedral : 12.215 156.836 1716 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 4.82 % Allowed : 24.94 % Favored : 70.24 % 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: 1.02 (0.29), residues: 1026 helix: 1.62 (0.20), residues: 746 sheet: None (None), residues: 0 loop : -1.97 (0.42), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 254 HIS 0.001 0.000 HIS A 209 PHE 0.004 0.001 PHE A 131 TYR 0.030 0.001 TYR A 455 ARG 0.008 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 146 time to evaluate : 0.852 Fit side-chains REVERT: A 62 TRP cc_start: 0.7647 (m100) cc_final: 0.7295 (m100) REVERT: A 116 ASP cc_start: 0.7724 (OUTLIER) cc_final: 0.7459 (t0) REVERT: A 182 TYR cc_start: 0.8033 (OUTLIER) cc_final: 0.7584 (m-10) REVERT: A 229 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8290 (mp) REVERT: A 318 MET cc_start: 0.7272 (ppp) cc_final: 0.6976 (ppp) REVERT: A 455 TYR cc_start: 0.6010 (p90) cc_final: 0.5769 (p90) REVERT: B 62 TRP cc_start: 0.7643 (m100) cc_final: 0.7349 (m100) REVERT: B 116 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.7430 (t0) REVERT: B 182 TYR cc_start: 0.8031 (OUTLIER) cc_final: 0.7579 (m-10) REVERT: B 229 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8294 (mp) REVERT: B 318 MET cc_start: 0.7272 (ppp) cc_final: 0.6963 (ppp) REVERT: B 455 TYR cc_start: 0.6009 (p90) cc_final: 0.5770 (p90) outliers start: 40 outliers final: 29 residues processed: 173 average time/residue: 0.1573 time to fit residues: 40.3821 Evaluate side-chains 175 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 140 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 431 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 10.0000 chunk 71 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 82 optimal weight: 0.0670 chunk 86 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 HIS A 491 ASN B 162 HIS B 491 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8528 Z= 0.184 Angle : 0.627 9.391 11660 Z= 0.298 Chirality : 0.041 0.241 1376 Planarity : 0.004 0.031 1370 Dihedral : 11.616 156.915 1716 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.98 % Allowed : 26.02 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.29), residues: 1026 helix: 1.59 (0.20), residues: 750 sheet: None (None), residues: 0 loop : -1.87 (0.43), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 254 HIS 0.001 0.000 HIS A 209 PHE 0.005 0.001 PHE B 258 TYR 0.032 0.001 TYR A 455 ARG 0.008 0.001 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 146 time to evaluate : 0.859 Fit side-chains REVERT: A 62 TRP cc_start: 0.7668 (m100) cc_final: 0.7289 (m100) REVERT: A 182 TYR cc_start: 0.8013 (OUTLIER) cc_final: 0.7518 (m-10) REVERT: A 229 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8288 (mp) REVERT: A 318 MET cc_start: 0.7273 (ppp) cc_final: 0.7003 (ppp) REVERT: A 455 TYR cc_start: 0.6100 (p90) cc_final: 0.5687 (p90) REVERT: B 62 TRP cc_start: 0.7625 (m100) cc_final: 0.7275 (m100) REVERT: B 182 TYR cc_start: 0.8011 (OUTLIER) cc_final: 0.7513 (m-10) REVERT: B 229 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8281 (mp) REVERT: B 318 MET cc_start: 0.7271 (ppp) cc_final: 0.6986 (ppp) REVERT: B 455 TYR cc_start: 0.6099 (p90) cc_final: 0.5692 (p90) REVERT: B 485 VAL cc_start: 0.8843 (p) cc_final: 0.8623 (p) outliers start: 33 outliers final: 28 residues processed: 166 average time/residue: 0.1672 time to fit residues: 41.1184 Evaluate side-chains 172 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 140 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 431 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 ASN B 491 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8528 Z= 0.197 Angle : 0.647 9.395 11660 Z= 0.306 Chirality : 0.042 0.241 1376 Planarity : 0.004 0.043 1370 Dihedral : 11.414 157.252 1716 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.98 % Allowed : 26.39 % Favored : 69.64 % 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: 0.98 (0.29), residues: 1026 helix: 1.54 (0.20), residues: 750 sheet: None (None), residues: 0 loop : -1.88 (0.43), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 254 HIS 0.001 0.000 HIS A 209 PHE 0.004 0.001 PHE A 140 TYR 0.030 0.001 TYR B 455 ARG 0.007 0.001 ARG B 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 141 time to evaluate : 0.973 Fit side-chains REVERT: A 62 TRP cc_start: 0.7711 (m100) cc_final: 0.7292 (m100) REVERT: A 229 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8297 (mp) REVERT: A 318 MET cc_start: 0.7276 (ppp) cc_final: 0.7009 (ppp) REVERT: A 455 TYR cc_start: 0.6096 (p90) cc_final: 0.5703 (p90) REVERT: B 62 TRP cc_start: 0.7669 (m100) cc_final: 0.7270 (m100) REVERT: B 229 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8298 (mp) REVERT: B 318 MET cc_start: 0.7273 (ppp) cc_final: 0.6998 (ppp) REVERT: B 455 TYR cc_start: 0.6102 (p90) cc_final: 0.5709 (p90) outliers start: 33 outliers final: 29 residues processed: 163 average time/residue: 0.1623 time to fit residues: 39.3432 Evaluate side-chains 170 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 139 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 431 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.8980 chunk 81 optimal weight: 0.0770 chunk 33 optimal weight: 0.9990 chunk 83 optimal weight: 0.1980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 4 optimal weight: 0.0970 chunk 58 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 ASN B 491 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.143256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.129251 restraints weight = 15290.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.131932 restraints weight = 8038.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.133822 restraints weight = 5082.434| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8528 Z= 0.171 Angle : 0.645 11.448 11660 Z= 0.302 Chirality : 0.041 0.241 1376 Planarity : 0.004 0.031 1370 Dihedral : 11.209 157.070 1716 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.01 % Allowed : 27.11 % Favored : 69.88 % 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: 1.08 (0.29), residues: 1026 helix: 1.62 (0.20), residues: 750 sheet: None (None), residues: 0 loop : -1.87 (0.42), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 254 HIS 0.001 0.000 HIS A 221 PHE 0.006 0.001 PHE B 118 TYR 0.031 0.001 TYR B 455 ARG 0.010 0.001 ARG A 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1753.37 seconds wall clock time: 33 minutes 1.62 seconds (1981.62 seconds total)