Starting phenix.real_space_refine on Fri Nov 15 04:25:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j74_36025/11_2024/8j74_36025.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j74_36025/11_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_36025/11_2024/8j74_36025.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j74_36025/11_2024/8j74_36025.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j74_36025/11_2024/8j74_36025.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j74_36025/11_2024/8j74_36025.cif" } 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. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8288 Number of models: 1 Model: "" Number of chains: 4 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: "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: "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: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 116 Unusual residues: {'AV0': 1, 'R16': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Restraints were copied for chains: B, F Time building chain proxies: 8.08, per 1000 atoms: 0.97 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 - 3.00 Amino acid : True - 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: 2.76 Conformation dependent library (CDL) restraints added in 994.0 milliseconds 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: 0.79 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: 2.61 Time building geometry restraints manager: 3.03 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: 0.00 - 1.68: 11209 1.68 - 3.36: 345 3.36 - 5.04: 70 5.04 - 6.72: 30 6.72 - 8.41: 6 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 3.040 nonbonded pdb=" OG SER A 34 " pdb=" OE1 GLU A 37 " model vdw 2.204 3.040 nonbonded pdb=" OG SER A 34 " pdb=" OE1 GLU A 36 " model vdw 2.232 3.040 nonbonded pdb=" OG SER B 34 " pdb=" OE1 GLU B 36 " model vdw 2.232 3.040 nonbonded pdb=" O PHE A 444 " pdb=" OG1 THR A 448 " model vdw 2.281 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 2.030 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 25.550 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.390 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.744 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: 0.1924 time to fit residues: 43.9656 Evaluate side-chains 144 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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: 1.9990 chunk 42 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 41 optimal weight: 0.4980 chunk 79 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 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: 0.8014 moved from start: 0.1059 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 : 0.753 10.131 11660 Z= 0.335 Chirality : 0.046 0.236 1376 Planarity : 0.004 0.028 1370 Dihedral : 19.397 148.671 1716 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.37 % Allowed : 22.65 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.29), residues: 1026 helix: 1.54 (0.20), residues: 742 sheet: None (None), residues: 0 loop : -1.92 (0.40), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 406 HIS 0.003 0.001 HIS A 221 PHE 0.010 0.001 PHE B 461 TYR 0.012 0.001 TYR A 414 ARG 0.005 0.001 ARG A 446 *********************** 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 174 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 TRP cc_start: 0.7843 (m100) cc_final: 0.7388 (m100) REVERT: A 130 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8791 (mp) REVERT: A 318 MET cc_start: 0.7113 (ppp) cc_final: 0.6446 (ppp) REVERT: A 455 TYR cc_start: 0.5472 (p90) cc_final: 0.5193 (p90) REVERT: B 62 TRP cc_start: 0.7843 (m100) cc_final: 0.7393 (m100) REVERT: B 130 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8785 (mp) REVERT: B 318 MET cc_start: 0.7110 (ppp) cc_final: 0.6428 (ppp) REVERT: B 455 TYR cc_start: 0.5467 (p90) cc_final: 0.5189 (p90) outliers start: 28 outliers final: 10 residues processed: 170 average time/residue: 0.1715 time to fit residues: 42.5185 Evaluate side-chains 144 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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 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 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: 0.9990 chunk 77 optimal weight: 7.9990 chunk 63 optimal weight: 0.0370 chunk 25 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- 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: 0.8002 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8528 Z= 0.180 Angle : 0.633 9.327 11660 Z= 0.298 Chirality : 0.042 0.236 1376 Planarity : 0.004 0.027 1370 Dihedral : 15.618 158.748 1716 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.86 % Allowed : 21.08 % Favored : 75.06 % 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: 1.53 (0.20), residues: 748 sheet: None (None), residues: 0 loop : -1.89 (0.42), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 300 HIS 0.001 0.000 HIS B 221 PHE 0.006 0.001 PHE A 140 TYR 0.015 0.001 TYR A 439 ARG 0.004 0.001 ARG A 38 *********************** 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 181 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 0.895 Fit side-chains REVERT: A 62 TRP cc_start: 0.7858 (m100) cc_final: 0.7352 (m100) REVERT: A 116 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7505 (t0) REVERT: A 318 MET cc_start: 0.7244 (ppp) cc_final: 0.6241 (ppp) REVERT: A 455 TYR cc_start: 0.5501 (p90) cc_final: 0.5211 (p90) REVERT: B 62 TRP cc_start: 0.7822 (m100) cc_final: 0.7312 (m100) REVERT: B 116 ASP cc_start: 0.7724 (OUTLIER) cc_final: 0.7402 (t0) REVERT: B 318 MET cc_start: 0.7242 (ppp) cc_final: 0.6224 (ppp) REVERT: B 455 TYR cc_start: 0.5498 (p90) cc_final: 0.5210 (p90) outliers start: 32 outliers final: 16 residues processed: 177 average time/residue: 0.1685 time to fit residues: 43.5521 Evaluate side-chains 153 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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 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 252 ILE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 116 ASP 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 252 ILE Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 368 PHE 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: 0.7980 chunk 10 optimal weight: 0.2980 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN A 365 GLN B 191 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1494 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= 0.179 Angle : 0.633 9.394 11660 Z= 0.296 Chirality : 0.042 0.241 1376 Planarity : 0.003 0.025 1370 Dihedral : 14.509 156.157 1716 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.61 % Allowed : 22.53 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.29), residues: 1026 helix: 1.58 (0.20), residues: 748 sheet: None (None), residues: 0 loop : -1.84 (0.42), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 300 HIS 0.001 0.000 HIS B 209 PHE 0.007 0.001 PHE B 131 TYR 0.012 0.001 TYR A 439 ARG 0.005 0.001 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 179 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 149 time to evaluate : 0.731 Fit side-chains REVERT: A 62 TRP cc_start: 0.7846 (m100) cc_final: 0.7631 (m100) REVERT: A 116 ASP cc_start: 0.7747 (OUTLIER) cc_final: 0.7521 (t0) REVERT: A 229 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8251 (mp) REVERT: A 318 MET cc_start: 0.6944 (ppp) cc_final: 0.6635 (ppp) REVERT: A 455 TYR cc_start: 0.5564 (p90) cc_final: 0.5256 (p90) REVERT: B 62 TRP cc_start: 0.7839 (m100) cc_final: 0.7626 (m100) REVERT: B 229 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8249 (mp) REVERT: B 318 MET cc_start: 0.6943 (ppp) cc_final: 0.6628 (ppp) REVERT: B 455 TYR cc_start: 0.5561 (p90) cc_final: 0.5257 (p90) outliers start: 30 outliers final: 22 residues processed: 175 average time/residue: 0.1671 time to fit residues: 42.6634 Evaluate side-chains 157 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.868 ------------------------------------------------------------------------------- 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 153 ILE 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 252 ILE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 368 PHE 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 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 229 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 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: 3.9990 chunk 73 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 84 optimal weight: 0.6980 chunk 68 optimal weight: 0.1980 chunk 0 optimal weight: 8.9990 chunk 50 optimal weight: 0.0770 chunk 88 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.9942 ------------------------------------------------------------------------------- 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: 0.8106 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8528 Z= 0.290 Angle : 0.681 9.371 11660 Z= 0.328 Chirality : 0.043 0.233 1376 Planarity : 0.004 0.026 1370 Dihedral : 13.860 155.296 1716 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.58 % Allowed : 23.49 % Favored : 71.93 % 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: 0.85 (0.29), residues: 1026 helix: 1.43 (0.20), residues: 748 sheet: None (None), residues: 0 loop : -1.85 (0.43), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 406 HIS 0.002 0.001 HIS B 209 PHE 0.010 0.001 PHE B 258 TYR 0.016 0.002 TYR A 439 ARG 0.007 0.001 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 172 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 134 time to evaluate : 0.861 Fit side-chains REVERT: A 229 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8369 (mp) REVERT: A 318 MET cc_start: 0.7272 (ppp) cc_final: 0.7009 (ppp) REVERT: A 455 TYR cc_start: 0.5697 (p90) cc_final: 0.5420 (p90) REVERT: B 229 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8367 (mp) REVERT: B 318 MET cc_start: 0.7273 (ppp) cc_final: 0.7001 (ppp) REVERT: B 455 TYR cc_start: 0.5695 (p90) cc_final: 0.5424 (p90) outliers start: 38 outliers final: 27 residues processed: 166 average time/residue: 0.1738 time to fit residues: 42.1630 Evaluate side-chains 155 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 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 153 ILE 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 427 VAL Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 115 LEU 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 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 427 VAL Chi-restraints excluded: chain B residue 431 ASN Chi-restraints excluded: chain B residue 485 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 0.0060 chunk 51 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- 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: 0.8045 moved from start: 0.1641 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= 0.182 Angle : 0.648 10.562 11660 Z= 0.304 Chirality : 0.041 0.238 1376 Planarity : 0.003 0.025 1370 Dihedral : 13.062 155.289 1716 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.98 % Allowed : 24.82 % Favored : 71.20 % 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: 1.50 (0.20), residues: 748 sheet: None (None), residues: 0 loop : -1.75 (0.44), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 300 HIS 0.000 0.000 HIS A 209 PHE 0.005 0.001 PHE A 140 TYR 0.013 0.001 TYR A 439 ARG 0.007 0.001 ARG A 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 176 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 143 time to evaluate : 0.935 Fit side-chains REVERT: A 116 ASP cc_start: 0.7919 (OUTLIER) cc_final: 0.7668 (t0) REVERT: A 229 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8347 (mp) REVERT: A 318 MET cc_start: 0.7265 (ppp) cc_final: 0.7031 (ppp) REVERT: A 455 TYR cc_start: 0.5761 (p90) cc_final: 0.5458 (p90) REVERT: B 229 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8345 (mp) REVERT: B 318 MET cc_start: 0.7264 (ppp) cc_final: 0.7023 (ppp) REVERT: B 455 TYR cc_start: 0.5756 (p90) cc_final: 0.5458 (p90) outliers start: 33 outliers final: 21 residues processed: 166 average time/residue: 0.1833 time to fit residues: 44.1397 Evaluate side-chains 161 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 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 427 VAL Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain A residue 485 VAL 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 330 VAL Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 431 ASN Chi-restraints excluded: chain B residue 485 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 83 optimal weight: 0.0870 chunk 98 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 39 optimal weight: 9.9990 chunk 58 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 overall best weight: 0.7358 ------------------------------------------------------------------------------- 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: 0.8036 moved from start: 0.1724 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= 0.183 Angle : 0.634 9.325 11660 Z= 0.299 Chirality : 0.042 0.234 1376 Planarity : 0.004 0.026 1370 Dihedral : 12.141 156.170 1716 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.86 % Allowed : 24.58 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.29), residues: 1026 helix: 1.53 (0.20), residues: 748 sheet: None (None), residues: 0 loop : -1.79 (0.43), residues: 278 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 0.007 0.001 PHE B 131 TYR 0.015 0.001 TYR B 439 ARG 0.007 0.001 ARG B 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 177 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 145 time to evaluate : 0.876 Fit side-chains REVERT: A 116 ASP cc_start: 0.7904 (OUTLIER) cc_final: 0.7661 (t0) REVERT: A 229 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8340 (mp) REVERT: A 318 MET cc_start: 0.7245 (ppp) cc_final: 0.7005 (ppp) REVERT: A 455 TYR cc_start: 0.5870 (p90) cc_final: 0.5359 (p90) REVERT: B 229 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8337 (mp) REVERT: B 318 MET cc_start: 0.7245 (ppp) cc_final: 0.6999 (ppp) REVERT: B 455 TYR cc_start: 0.5865 (p90) cc_final: 0.5354 (p90) outliers start: 32 outliers final: 21 residues processed: 164 average time/residue: 0.1723 time to fit residues: 40.9019 Evaluate side-chains 161 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.885 ------------------------------------------------------------------------------- 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 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 431 ASN Chi-restraints excluded: chain A residue 485 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 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 431 ASN Chi-restraints excluded: chain B residue 485 VAL 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: 0.4980 chunk 66 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.8036 moved from start: 0.1746 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= 0.192 Angle : 0.659 12.064 11660 Z= 0.307 Chirality : 0.042 0.235 1376 Planarity : 0.004 0.038 1370 Dihedral : 11.784 156.776 1716 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.01 % Allowed : 26.02 % Favored : 70.96 % 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: 1.51 (0.20), residues: 748 sheet: None (None), residues: 0 loop : -1.80 (0.43), residues: 278 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 0.006 0.001 PHE A 131 TYR 0.014 0.001 TYR B 439 ARG 0.008 0.001 ARG B 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 167 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.905 Fit side-chains REVERT: A 116 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7634 (t0) REVERT: A 229 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8332 (mp) REVERT: A 318 MET cc_start: 0.7213 (ppp) cc_final: 0.7002 (ppp) REVERT: A 455 TYR cc_start: 0.5957 (p90) cc_final: 0.5440 (p90) REVERT: B 229 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8326 (mp) REVERT: B 318 MET cc_start: 0.7210 (ppp) cc_final: 0.6994 (ppp) REVERT: B 455 TYR cc_start: 0.5950 (p90) cc_final: 0.5430 (p90) outliers start: 25 outliers final: 20 residues processed: 155 average time/residue: 0.1803 time to fit residues: 40.1350 Evaluate side-chains 161 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 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 431 ASN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 100 LEU 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 330 VAL Chi-restraints excluded: chain B residue 368 PHE 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: 9.9990 chunk 71 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 82 optimal weight: 0.0370 chunk 86 optimal weight: 6.9990 chunk 91 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 96 optimal weight: 0.0040 chunk 59 optimal weight: 0.9980 chunk 45 optimal weight: 0.0970 chunk 67 optimal weight: 1.9990 overall best weight: 0.3268 ------------------------------------------------------------------------------- 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: 0.7980 moved from start: 0.1809 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= 0.166 Angle : 0.629 9.376 11660 Z= 0.295 Chirality : 0.041 0.237 1376 Planarity : 0.003 0.026 1370 Dihedral : 11.425 157.349 1716 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.41 % Allowed : 26.63 % Favored : 70.96 % 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: 1.04 (0.29), residues: 1026 helix: 1.56 (0.20), residues: 750 sheet: None (None), residues: 0 loop : -1.79 (0.42), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 300 HIS 0.001 0.000 HIS B 221 PHE 0.006 0.001 PHE A 131 TYR 0.015 0.001 TYR B 439 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 177 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 0.915 Fit side-chains REVERT: A 116 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7558 (t0) REVERT: A 318 MET cc_start: 0.7230 (ppp) cc_final: 0.6886 (ppp) REVERT: A 455 TYR cc_start: 0.5955 (p90) cc_final: 0.5444 (p90) REVERT: A 485 VAL cc_start: 0.8817 (p) cc_final: 0.8614 (p) REVERT: B 318 MET cc_start: 0.7226 (ppp) cc_final: 0.6885 (ppp) REVERT: B 455 TYR cc_start: 0.5948 (p90) cc_final: 0.5435 (p90) REVERT: B 485 VAL cc_start: 0.8816 (p) cc_final: 0.8613 (p) outliers start: 20 outliers final: 18 residues processed: 170 average time/residue: 0.1742 time to fit residues: 43.0707 Evaluate side-chains 165 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 184 VAL 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 431 ASN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 100 LEU 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 252 ILE Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 368 PHE 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: 0.9990 chunk 93 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 62 optimal weight: 0.1980 chunk 49 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 11 optimal weight: 0.0570 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1896 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= 0.186 Angle : 0.641 9.409 11660 Z= 0.302 Chirality : 0.042 0.239 1376 Planarity : 0.003 0.035 1370 Dihedral : 11.326 158.549 1716 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.29 % Allowed : 27.35 % Favored : 70.36 % 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: 1.04 (0.29), residues: 1026 helix: 1.58 (0.20), residues: 748 sheet: None (None), residues: 0 loop : -1.84 (0.42), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 254 HIS 0.001 0.000 HIS A 209 PHE 0.007 0.001 PHE B 131 TYR 0.016 0.001 TYR A 439 ARG 0.008 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 171 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.892 Fit side-chains REVERT: A 318 MET cc_start: 0.7304 (ppp) cc_final: 0.7087 (ppp) REVERT: A 455 TYR cc_start: 0.6051 (p90) cc_final: 0.5540 (p90) REVERT: B 318 MET cc_start: 0.7292 (ppp) cc_final: 0.7073 (ppp) REVERT: B 455 TYR cc_start: 0.6046 (p90) cc_final: 0.5533 (p90) outliers start: 19 outliers final: 18 residues processed: 165 average time/residue: 0.1755 time to fit residues: 41.7499 Evaluate side-chains 163 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 130 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 184 VAL 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 431 ASN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 100 LEU 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 252 ILE Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 368 PHE 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: 0.9990 chunk 81 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 83 optimal weight: 0.0570 chunk 10 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.143040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.129257 restraints weight = 15198.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.132015 restraints weight = 7761.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.133722 restraints weight = 4794.609| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8528 Z= 0.196 Angle : 0.662 13.144 11660 Z= 0.311 Chirality : 0.042 0.240 1376 Planarity : 0.004 0.042 1370 Dihedral : 11.285 158.823 1716 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.53 % Allowed : 26.75 % Favored : 70.72 % 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: 1.53 (0.20), residues: 748 sheet: None (None), residues: 0 loop : -1.85 (0.43), residues: 278 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 0.006 0.001 PHE B 131 TYR 0.024 0.001 TYR B 305 ARG 0.008 0.001 ARG B 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1771.83 seconds wall clock time: 33 minutes 25.02 seconds (2005.02 seconds total)