Starting phenix.real_space_refine on Tue Jun 25 10:38:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tti_26116/06_2024/7tti_26116_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tti_26116/06_2024/7tti_26116.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tti_26116/06_2024/7tti_26116.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tti_26116/06_2024/7tti_26116.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tti_26116/06_2024/7tti_26116_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tti_26116/06_2024/7tti_26116_trim_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.043 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 62 5.16 5 C 5030 2.51 5 N 1208 2.21 5 O 1370 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 222": "OE1" <-> "OE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 7670 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 3753 Classifications: {'peptide': 542} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 27, 'TRANS': 514} Unresolved non-hydrogen bonds: 370 Unresolved non-hydrogen angles: 464 Unresolved non-hydrogen dihedrals: 316 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 11, 'TYR:plan': 5, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 7, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 233 Chain: "B" Number of atoms: 3753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 3753 Classifications: {'peptide': 542} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 27, 'TRANS': 514} Unresolved non-hydrogen bonds: 370 Unresolved non-hydrogen angles: 464 Unresolved non-hydrogen dihedrals: 316 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 11, 'TYR:plan': 5, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 7, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 233 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'JUX': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'JUX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.49, per 1000 atoms: 0.72 Number of scatterers: 7670 At special positions: 0 Unit cell: (85.905, 108.675, 104.535, 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 62 16.00 O 1370 8.00 N 1208 7.00 C 5030 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 626 " distance=2.03 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 353 " distance=2.03 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 626 " distance=2.03 Simple disulfide: pdb=" SG CYS B 308 " - pdb=" SG CYS B 323 " distance=2.03 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 353 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN A 312 " " NAG D 1 " - " ASN A 361 " " NAG E 1 " - " ASN B 312 " " NAG F 1 " - " ASN B 361 " Time building additional restraints: 4.52 Conformation dependent library (CDL) restraints added in 1.6 seconds 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1984 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 2 sheets defined 62.9% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 121 through 133 removed outlier: 4.442A pdb=" N LEU A 126 " --> pdb=" O MET A 122 " (cutoff:3.500A) Proline residue: A 127 - end of helix removed outlier: 3.522A pdb=" N PHE A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 177 removed outlier: 6.586A pdb=" N VAL A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N LEU A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASN A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 192 Processing helix chain 'A' and resid 195 through 226 removed outlier: 3.841A pdb=" N ALA A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 Proline residue: A 237 - end of helix Processing helix chain 'A' and resid 244 through 267 removed outlier: 3.849A pdb=" N THR A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE A 261 " --> pdb=" O ILE A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 274 through 300 Processing helix chain 'A' and resid 337 through 340 No H-bonds generated for 'chain 'A' and resid 337 through 340' Processing helix chain 'A' and resid 355 through 359 Processing helix chain 'A' and resid 373 through 378 Processing helix chain 'A' and resid 420 through 431 Proline residue: A 429 - end of helix Processing helix chain 'A' and resid 436 through 439 No H-bonds generated for 'chain 'A' and resid 436 through 439' Processing helix chain 'A' and resid 447 through 449 No H-bonds generated for 'chain 'A' and resid 447 through 449' Processing helix chain 'A' and resid 451 through 476 Processing helix chain 'A' and resid 479 through 482 No H-bonds generated for 'chain 'A' and resid 479 through 482' Processing helix chain 'A' and resid 485 through 487 No H-bonds generated for 'chain 'A' and resid 485 through 487' Processing helix chain 'A' and resid 495 through 499 removed outlier: 3.569A pdb=" N LEU A 499 " --> pdb=" O VAL A 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 495 through 499' Processing helix chain 'A' and resid 504 through 535 Proline residue: A 527 - end of helix Processing helix chain 'A' and resid 540 through 542 No H-bonds generated for 'chain 'A' and resid 540 through 542' Processing helix chain 'A' and resid 550 through 552 No H-bonds generated for 'chain 'A' and resid 550 through 552' Processing helix chain 'A' and resid 558 through 571 Processing helix chain 'A' and resid 579 through 601 Processing helix chain 'A' and resid 614 through 655 removed outlier: 4.254A pdb=" N MET A 630 " --> pdb=" O CYS A 626 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N TYR A 636 " --> pdb=" O VAL A 632 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N TYR A 637 " --> pdb=" O SER A 633 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL A 640 " --> pdb=" O TYR A 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 133 removed outlier: 4.428A pdb=" N LEU B 126 " --> pdb=" O MET B 122 " (cutoff:3.500A) Proline residue: B 127 - end of helix Processing helix chain 'B' and resid 140 through 177 removed outlier: 6.569A pdb=" N VAL B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N LEU B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN B 152 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASN B 177 " --> pdb=" O ALA B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 195 through 226 removed outlier: 3.763A pdb=" N ALA B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 239 Proline residue: B 237 - end of helix Processing helix chain 'B' and resid 244 through 267 removed outlier: 3.866A pdb=" N THR B 256 " --> pdb=" O ARG B 252 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE B 261 " --> pdb=" O ILE B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' Processing helix chain 'B' and resid 274 through 300 Processing helix chain 'B' and resid 337 through 340 No H-bonds generated for 'chain 'B' and resid 337 through 340' Processing helix chain 'B' and resid 355 through 359 Processing helix chain 'B' and resid 373 through 378 Processing helix chain 'B' and resid 420 through 431 Proline residue: B 429 - end of helix Processing helix chain 'B' and resid 436 through 439 No H-bonds generated for 'chain 'B' and resid 436 through 439' Processing helix chain 'B' and resid 447 through 449 No H-bonds generated for 'chain 'B' and resid 447 through 449' Processing helix chain 'B' and resid 451 through 476 Processing helix chain 'B' and resid 479 through 482 No H-bonds generated for 'chain 'B' and resid 479 through 482' Processing helix chain 'B' and resid 485 through 487 No H-bonds generated for 'chain 'B' and resid 485 through 487' Processing helix chain 'B' and resid 495 through 499 removed outlier: 3.564A pdb=" N LEU B 499 " --> pdb=" O VAL B 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 495 through 499' Processing helix chain 'B' and resid 504 through 535 Proline residue: B 527 - end of helix Processing helix chain 'B' and resid 540 through 542 No H-bonds generated for 'chain 'B' and resid 540 through 542' Processing helix chain 'B' and resid 550 through 552 No H-bonds generated for 'chain 'B' and resid 550 through 552' Processing helix chain 'B' and resid 558 through 571 Processing helix chain 'B' and resid 579 through 601 Processing helix chain 'B' and resid 614 through 655 removed outlier: 4.249A pdb=" N MET B 630 " --> pdb=" O CYS B 626 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N TYR B 636 " --> pdb=" O VAL B 632 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N TYR B 637 " --> pdb=" O SER B 633 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL B 640 " --> pdb=" O TYR B 636 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 306 through 310 Processing sheet with id= B, first strand: chain 'B' and resid 306 through 310 459 hydrogen bonds defined for protein. 1371 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: 2.18 Time building geometry restraints manager: 4.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2346 1.34 - 1.46: 1915 1.46 - 1.58: 3503 1.58 - 1.70: 0 1.70 - 1.82: 88 Bond restraints: 7852 Sorted by residual: bond pdb=" C5 JUX B1201 " pdb=" S1 JUX B1201 " ideal model delta sigma weight residual 1.734 1.400 0.334 2.00e-02 2.50e+03 2.80e+02 bond pdb=" C5 JUX A1201 " pdb=" S1 JUX A1201 " ideal model delta sigma weight residual 1.734 1.400 0.334 2.00e-02 2.50e+03 2.79e+02 bond pdb=" C8 JUX A1201 " pdb=" S1 JUX A1201 " ideal model delta sigma weight residual 1.721 1.394 0.327 2.00e-02 2.50e+03 2.67e+02 bond pdb=" C8 JUX B1201 " pdb=" S1 JUX B1201 " ideal model delta sigma weight residual 1.721 1.394 0.327 2.00e-02 2.50e+03 2.67e+02 bond pdb=" C9 JUX A1201 " pdb=" S2 JUX A1201 " ideal model delta sigma weight residual 1.823 1.745 0.078 2.00e-02 2.50e+03 1.52e+01 ... (remaining 7847 not shown) Histogram of bond angle deviations from ideal: 58.91 - 74.11: 6 74.11 - 89.31: 0 89.31 - 104.52: 158 104.52 - 119.72: 6650 119.72 - 134.92: 3990 Bond angle restraints: 10804 Sorted by residual: angle pdb=" C7 JUX A1201 " pdb=" C6 JUX A1201 " pdb=" N2 JUX A1201 " ideal model delta sigma weight residual 119.28 134.92 -15.64 3.00e+00 1.11e-01 2.72e+01 angle pdb=" C7 JUX B1201 " pdb=" C6 JUX B1201 " pdb=" N2 JUX B1201 " ideal model delta sigma weight residual 119.28 134.81 -15.53 3.00e+00 1.11e-01 2.68e+01 angle pdb=" N JUX A1201 " pdb=" CA JUX A1201 " pdb=" C JUX A1201 " ideal model delta sigma weight residual 119.72 108.51 11.21 3.00e+00 1.11e-01 1.40e+01 angle pdb=" N JUX B1201 " pdb=" CA JUX B1201 " pdb=" C JUX B1201 " ideal model delta sigma weight residual 119.72 108.96 10.76 3.00e+00 1.11e-01 1.29e+01 angle pdb=" N ILE A 538 " pdb=" CA ILE A 538 " pdb=" C ILE A 538 " ideal model delta sigma weight residual 111.81 108.78 3.03 8.60e-01 1.35e+00 1.24e+01 ... (remaining 10799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.81: 4279 22.81 - 45.61: 277 45.61 - 68.41: 44 68.41 - 91.22: 18 91.22 - 114.02: 8 Dihedral angle restraints: 4626 sinusoidal: 1526 harmonic: 3100 Sorted by residual: dihedral pdb=" CA CYS B 626 " pdb=" C CYS B 626 " pdb=" N LEU B 627 " pdb=" CA LEU B 627 " ideal model delta harmonic sigma weight residual 180.00 146.56 33.44 0 5.00e+00 4.00e-02 4.47e+01 dihedral pdb=" CA CYS A 626 " pdb=" C CYS A 626 " pdb=" N LEU A 627 " pdb=" CA LEU A 627 " ideal model delta harmonic sigma weight residual 180.00 146.63 33.37 0 5.00e+00 4.00e-02 4.45e+01 dihedral pdb=" CB CYS A 308 " pdb=" SG CYS A 308 " pdb=" SG CYS A 323 " pdb=" CB CYS A 323 " ideal model delta sinusoidal sigma weight residual -86.00 -133.74 47.74 1 1.00e+01 1.00e-02 3.14e+01 ... (remaining 4623 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1011 0.037 - 0.074: 276 0.074 - 0.111: 77 0.111 - 0.149: 12 0.149 - 0.186: 2 Chirality restraints: 1378 Sorted by residual: chirality pdb=" CA CYS B 626 " pdb=" N CYS B 626 " pdb=" C CYS B 626 " pdb=" CB CYS B 626 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.62e-01 chirality pdb=" CA CYS A 626 " pdb=" N CYS A 626 " pdb=" C CYS A 626 " pdb=" CB CYS A 626 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.19 2.00e-01 2.50e+01 8.57e-01 chirality pdb=" CA JUX B1201 " pdb=" N JUX B1201 " pdb=" C JUX B1201 " pdb=" C4 JUX B1201 " both_signs ideal model delta sigma weight residual True 2.30 -2.44 -0.14 2.00e-01 2.50e+01 4.90e-01 ... (remaining 1375 not shown) Planarity restraints: 1332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N JUX B1201 " 0.122 2.00e-02 2.50e+03 9.89e-02 1.47e+02 pdb=" CA JUX B1201 " -0.138 2.00e-02 2.50e+03 pdb=" OH JUX B1201 " -0.131 2.00e-02 2.50e+03 pdb=" C1 JUX B1201 " 0.038 2.00e-02 2.50e+03 pdb=" C5 JUX B1201 " 0.042 2.00e-02 2.50e+03 pdb=" C9 JUX B1201 " 0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N JUX A1201 " -0.109 2.00e-02 2.50e+03 9.67e-02 1.40e+02 pdb=" CA JUX A1201 " 0.135 2.00e-02 2.50e+03 pdb=" OH JUX A1201 " 0.130 2.00e-02 2.50e+03 pdb=" C1 JUX A1201 " -0.033 2.00e-02 2.50e+03 pdb=" C5 JUX A1201 " -0.051 2.00e-02 2.50e+03 pdb=" C9 JUX A1201 " -0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 236 " -0.025 5.00e-02 4.00e+02 3.89e-02 2.43e+00 pdb=" N PRO A 237 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 237 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 237 " -0.022 5.00e-02 4.00e+02 ... (remaining 1329 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 63 2.57 - 3.15: 7567 3.15 - 3.74: 12592 3.74 - 4.32: 14991 4.32 - 4.90: 25341 Nonbonded interactions: 60554 Sorted by model distance: nonbonded pdb=" OH TYR B 292 " pdb=" OG SER B 468 " model vdw 1.990 2.440 nonbonded pdb=" OH TYR A 292 " pdb=" OG SER A 468 " model vdw 1.995 2.440 nonbonded pdb=" OG SER A 345 " pdb=" OD1 ASN A 347 " model vdw 1.997 2.440 nonbonded pdb=" OG SER B 345 " pdb=" OD1 ASN B 347 " model vdw 1.999 2.440 nonbonded pdb=" O6 NAG F 1 " pdb=" O5 NAG F 2 " model vdw 2.093 2.440 ... (remaining 60549 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = 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: 1.200 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: 4.900 Check model and map are aligned: 0.000 Set scattering table: 0.070 Process input model: 28.660 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.070 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6192 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 : 0.008 0.334 7852 Z= 0.526 Angle : 0.627 15.643 10804 Z= 0.280 Chirality : 0.038 0.186 1378 Planarity : 0.005 0.099 1328 Dihedral : 16.783 114.025 2624 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 50.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 0.28 % Allowed : 17.98 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.28), residues: 1080 helix: 3.18 (0.21), residues: 626 sheet: None (None), residues: 0 loop : -1.75 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 616 HIS 0.001 0.000 HIS A 344 PHE 0.007 0.001 PHE A 541 TYR 0.006 0.001 TYR A 186 ARG 0.001 0.000 ARG A 140 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 198 time to evaluate : 0.693 Fit side-chains REVERT: A 410 LEU cc_start: 0.7355 (mt) cc_final: 0.6821 (tp) REVERT: A 571 ILE cc_start: 0.7071 (mm) cc_final: 0.6725 (mt) REVERT: A 583 MET cc_start: 0.7334 (mmm) cc_final: 0.6946 (mmm) REVERT: B 357 PHE cc_start: 0.5113 (m-80) cc_final: 0.4851 (t80) REVERT: B 410 LEU cc_start: 0.7478 (mt) cc_final: 0.7037 (tp) REVERT: B 411 TYR cc_start: 0.8196 (m-10) cc_final: 0.7992 (m-80) REVERT: B 528 ARG cc_start: 0.7469 (mpt-90) cc_final: 0.7259 (mmt90) REVERT: B 571 ILE cc_start: 0.7164 (mm) cc_final: 0.6844 (mt) REVERT: B 583 MET cc_start: 0.7313 (mmm) cc_final: 0.6864 (mmm) REVERT: B 643 LEU cc_start: 0.6008 (OUTLIER) cc_final: 0.5802 (mt) outliers start: 2 outliers final: 0 residues processed: 200 average time/residue: 0.1450 time to fit residues: 42.0181 Evaluate side-chains 130 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 129 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 643 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.0470 chunk 81 optimal weight: 7.9990 chunk 45 optimal weight: 0.0060 chunk 27 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 0.0060 chunk 84 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 overall best weight: 0.3510 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 ASN B 250 ASN B 347 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6258 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7852 Z= 0.221 Angle : 0.712 8.631 10804 Z= 0.339 Chirality : 0.046 0.213 1378 Planarity : 0.005 0.057 1328 Dihedral : 13.685 97.897 1326 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 4.49 % Allowed : 21.91 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.27), residues: 1080 helix: 2.46 (0.21), residues: 626 sheet: None (None), residues: 0 loop : -1.71 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 339 HIS 0.001 0.000 HIS B 394 PHE 0.014 0.002 PHE B 205 TYR 0.010 0.001 TYR A 637 ARG 0.003 0.001 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 151 time to evaluate : 0.763 Fit side-chains REVERT: A 490 VAL cc_start: 0.6399 (OUTLIER) cc_final: 0.6054 (p) REVERT: A 571 ILE cc_start: 0.7434 (mm) cc_final: 0.7082 (mt) REVERT: B 130 GLN cc_start: 0.8107 (tm-30) cc_final: 0.7835 (tm-30) REVERT: B 411 TYR cc_start: 0.8122 (m-10) cc_final: 0.7896 (m-80) REVERT: B 571 ILE cc_start: 0.7401 (mm) cc_final: 0.7077 (mt) outliers start: 32 outliers final: 21 residues processed: 171 average time/residue: 0.1608 time to fit residues: 39.0786 Evaluate side-chains 161 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 139 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 507 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 87 optimal weight: 0.0000 chunk 97 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6289 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7852 Z= 0.233 Angle : 0.669 9.434 10804 Z= 0.317 Chirality : 0.044 0.212 1378 Planarity : 0.005 0.050 1328 Dihedral : 12.797 92.136 1324 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 6.46 % Allowed : 21.91 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.27), residues: 1080 helix: 2.31 (0.21), residues: 618 sheet: 2.14 (1.06), residues: 20 loop : -1.88 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 501 HIS 0.001 0.000 HIS B 344 PHE 0.020 0.001 PHE A 591 TYR 0.006 0.001 TYR A 186 ARG 0.003 0.001 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 146 time to evaluate : 0.820 Fit side-chains REVERT: A 137 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7424 (tp) REVERT: A 223 ILE cc_start: 0.5930 (mm) cc_final: 0.5655 (mm) REVERT: A 490 VAL cc_start: 0.6449 (OUTLIER) cc_final: 0.6101 (p) REVERT: A 571 ILE cc_start: 0.7632 (mm) cc_final: 0.7348 (mt) REVERT: B 137 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7368 (tp) REVERT: B 223 ILE cc_start: 0.6042 (mm) cc_final: 0.5768 (mm) REVERT: B 411 TYR cc_start: 0.8046 (m-80) cc_final: 0.7645 (m-80) REVERT: B 571 ILE cc_start: 0.7692 (mm) cc_final: 0.7408 (mt) outliers start: 46 outliers final: 26 residues processed: 178 average time/residue: 0.1390 time to fit residues: 36.5663 Evaluate side-chains 168 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 139 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 619 SER Chi-restraints excluded: chain B residue 654 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 10 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6309 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7852 Z= 0.239 Angle : 0.659 9.657 10804 Z= 0.316 Chirality : 0.044 0.244 1378 Planarity : 0.005 0.055 1328 Dihedral : 12.062 85.832 1324 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 7.44 % Allowed : 21.21 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.27), residues: 1080 helix: 2.22 (0.21), residues: 620 sheet: None (None), residues: 0 loop : -1.74 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 339 HIS 0.002 0.000 HIS A 394 PHE 0.022 0.002 PHE B 591 TYR 0.008 0.001 TYR B 411 ARG 0.003 0.001 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 141 time to evaluate : 0.771 Fit side-chains REVERT: A 137 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7439 (tp) REVERT: A 490 VAL cc_start: 0.6521 (OUTLIER) cc_final: 0.6165 (p) REVERT: A 571 ILE cc_start: 0.7607 (mm) cc_final: 0.7310 (mt) REVERT: A 630 MET cc_start: 0.6421 (OUTLIER) cc_final: 0.6189 (ptm) REVERT: B 137 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7443 (tp) REVERT: B 571 ILE cc_start: 0.7770 (mm) cc_final: 0.7505 (mt) REVERT: B 654 TYR cc_start: 0.4860 (OUTLIER) cc_final: 0.3640 (t80) outliers start: 53 outliers final: 33 residues processed: 182 average time/residue: 0.1453 time to fit residues: 38.3914 Evaluate side-chains 170 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 132 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 619 SER Chi-restraints excluded: chain B residue 654 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.0970 chunk 59 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 77 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6301 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7852 Z= 0.211 Angle : 0.652 9.665 10804 Z= 0.307 Chirality : 0.043 0.253 1378 Planarity : 0.005 0.056 1328 Dihedral : 11.548 81.349 1324 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 6.32 % Allowed : 23.46 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.27), residues: 1080 helix: 2.23 (0.21), residues: 622 sheet: None (None), residues: 0 loop : -1.71 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 339 HIS 0.001 0.000 HIS B 394 PHE 0.021 0.001 PHE A 591 TYR 0.006 0.001 TYR A 186 ARG 0.003 0.001 ARG B 528 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 136 time to evaluate : 0.817 Fit side-chains REVERT: A 137 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7505 (tp) REVERT: A 155 LEU cc_start: 0.6117 (OUTLIER) cc_final: 0.5779 (tt) REVERT: A 490 VAL cc_start: 0.6520 (OUTLIER) cc_final: 0.6176 (p) REVERT: A 556 TRP cc_start: 0.5236 (m100) cc_final: 0.4450 (m-10) REVERT: A 571 ILE cc_start: 0.7590 (mm) cc_final: 0.7283 (mt) REVERT: A 630 MET cc_start: 0.6368 (OUTLIER) cc_final: 0.6154 (ptm) REVERT: A 654 TYR cc_start: 0.4877 (OUTLIER) cc_final: 0.3655 (t80) REVERT: B 137 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7416 (tp) REVERT: B 556 TRP cc_start: 0.5265 (m100) cc_final: 0.4453 (m-10) REVERT: B 571 ILE cc_start: 0.7734 (mm) cc_final: 0.7466 (mt) REVERT: B 630 MET cc_start: 0.6316 (OUTLIER) cc_final: 0.6094 (ptm) REVERT: B 654 TYR cc_start: 0.4942 (OUTLIER) cc_final: 0.3705 (t80) outliers start: 45 outliers final: 29 residues processed: 169 average time/residue: 0.1395 time to fit residues: 34.6956 Evaluate side-chains 168 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 131 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain B residue 654 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 20 optimal weight: 0.0570 chunk 61 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- 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: 0.6319 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7852 Z= 0.232 Angle : 0.655 9.767 10804 Z= 0.310 Chirality : 0.044 0.262 1378 Planarity : 0.005 0.056 1328 Dihedral : 11.136 88.694 1324 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 7.58 % Allowed : 22.61 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.27), residues: 1080 helix: 2.22 (0.21), residues: 620 sheet: None (None), residues: 0 loop : -1.69 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 501 HIS 0.001 0.000 HIS B 344 PHE 0.020 0.001 PHE A 591 TYR 0.007 0.001 TYR A 186 ARG 0.002 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 132 time to evaluate : 0.715 Fit side-chains REVERT: A 137 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7550 (tp) REVERT: A 155 LEU cc_start: 0.6168 (OUTLIER) cc_final: 0.5824 (tt) REVERT: A 248 LEU cc_start: 0.5792 (OUTLIER) cc_final: 0.5585 (mp) REVERT: A 556 TRP cc_start: 0.5273 (m100) cc_final: 0.4492 (m-10) REVERT: A 571 ILE cc_start: 0.7604 (mm) cc_final: 0.7307 (mt) REVERT: A 630 MET cc_start: 0.6387 (OUTLIER) cc_final: 0.6115 (ptm) REVERT: A 654 TYR cc_start: 0.4801 (OUTLIER) cc_final: 0.3600 (t80) REVERT: B 137 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7491 (tp) REVERT: B 155 LEU cc_start: 0.6121 (OUTLIER) cc_final: 0.5788 (tt) REVERT: B 556 TRP cc_start: 0.5262 (m100) cc_final: 0.4442 (m-10) REVERT: B 571 ILE cc_start: 0.7716 (mm) cc_final: 0.7451 (mt) REVERT: B 654 TYR cc_start: 0.4807 (OUTLIER) cc_final: 0.3611 (t80) outliers start: 54 outliers final: 38 residues processed: 175 average time/residue: 0.1404 time to fit residues: 36.4842 Evaluate side-chains 175 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 129 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 344 HIS Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 619 SER Chi-restraints excluded: chain B residue 654 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.0470 chunk 11 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 87 optimal weight: 0.0170 chunk 58 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.4316 ------------------------------------------------------------------------------- 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: 0.6295 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7852 Z= 0.202 Angle : 0.653 9.742 10804 Z= 0.305 Chirality : 0.043 0.261 1378 Planarity : 0.005 0.056 1328 Dihedral : 10.690 88.257 1324 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 5.90 % Allowed : 25.00 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.27), residues: 1080 helix: 2.29 (0.21), residues: 620 sheet: None (None), residues: 0 loop : -1.69 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 339 HIS 0.000 0.000 HIS B 344 PHE 0.016 0.001 PHE B 591 TYR 0.005 0.001 TYR A 186 ARG 0.001 0.000 ARG B 252 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 129 time to evaluate : 0.817 Fit side-chains REVERT: A 137 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7514 (tp) REVERT: A 155 LEU cc_start: 0.6093 (OUTLIER) cc_final: 0.5766 (tt) REVERT: A 556 TRP cc_start: 0.5242 (m100) cc_final: 0.4469 (m-10) REVERT: A 571 ILE cc_start: 0.7563 (mm) cc_final: 0.7248 (mt) REVERT: A 654 TYR cc_start: 0.4734 (OUTLIER) cc_final: 0.3574 (t80) REVERT: B 137 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7441 (tp) REVERT: B 155 LEU cc_start: 0.6155 (OUTLIER) cc_final: 0.5821 (tt) REVERT: B 556 TRP cc_start: 0.5338 (m100) cc_final: 0.4471 (m-10) REVERT: B 571 ILE cc_start: 0.7630 (mm) cc_final: 0.7353 (mt) REVERT: B 654 TYR cc_start: 0.4787 (OUTLIER) cc_final: 0.3596 (t80) outliers start: 42 outliers final: 30 residues processed: 165 average time/residue: 0.1413 time to fit residues: 34.4501 Evaluate side-chains 162 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 126 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 631 PHE Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 654 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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: 0.6355 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7852 Z= 0.285 Angle : 0.693 9.885 10804 Z= 0.326 Chirality : 0.045 0.259 1378 Planarity : 0.005 0.057 1328 Dihedral : 10.296 88.363 1324 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 6.32 % Allowed : 24.58 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.27), residues: 1080 helix: 2.10 (0.21), residues: 622 sheet: None (None), residues: 0 loop : -1.71 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 501 HIS 0.001 0.000 HIS B 394 PHE 0.025 0.002 PHE B 591 TYR 0.007 0.001 TYR A 186 ARG 0.003 0.000 ARG B 528 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 128 time to evaluate : 0.824 Fit side-chains REVERT: A 137 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7696 (tp) REVERT: A 571 ILE cc_start: 0.7561 (mm) cc_final: 0.7270 (mt) REVERT: B 137 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7647 (tp) REVERT: B 571 ILE cc_start: 0.7763 (mm) cc_final: 0.7511 (mt) REVERT: B 654 TYR cc_start: 0.4712 (OUTLIER) cc_final: 0.3604 (t80) outliers start: 45 outliers final: 35 residues processed: 165 average time/residue: 0.1840 time to fit residues: 44.2571 Evaluate side-chains 158 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 120 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 344 HIS Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 654 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 2.9990 chunk 97 optimal weight: 0.0570 chunk 99 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 29 optimal weight: 0.0270 chunk 87 optimal weight: 0.0170 chunk 91 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.3394 ------------------------------------------------------------------------------- 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: 0.6290 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7852 Z= 0.196 Angle : 0.674 9.934 10804 Z= 0.312 Chirality : 0.043 0.249 1378 Planarity : 0.005 0.057 1328 Dihedral : 9.768 87.291 1324 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 5.48 % Allowed : 25.70 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.27), residues: 1080 helix: 2.25 (0.21), residues: 620 sheet: None (None), residues: 0 loop : -1.73 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 501 HIS 0.000 0.000 HIS B 394 PHE 0.018 0.001 PHE B 591 TYR 0.005 0.001 TYR B 186 ARG 0.002 0.001 ARG B 440 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 125 time to evaluate : 0.759 Fit side-chains REVERT: A 137 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7652 (tp) REVERT: A 410 LEU cc_start: 0.7119 (tp) cc_final: 0.6859 (tp) REVERT: A 556 TRP cc_start: 0.5282 (m100) cc_final: 0.4528 (m-10) REVERT: A 571 ILE cc_start: 0.7517 (mm) cc_final: 0.7193 (mt) REVERT: A 573 SER cc_start: 0.6567 (t) cc_final: 0.6265 (t) REVERT: A 654 TYR cc_start: 0.4728 (OUTLIER) cc_final: 0.3579 (t80) REVERT: B 137 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7634 (tp) REVERT: B 556 TRP cc_start: 0.5301 (m100) cc_final: 0.4531 (m-10) REVERT: B 571 ILE cc_start: 0.7543 (mm) cc_final: 0.7223 (mt) REVERT: B 654 TYR cc_start: 0.4701 (OUTLIER) cc_final: 0.3599 (t80) outliers start: 39 outliers final: 32 residues processed: 161 average time/residue: 0.1425 time to fit residues: 33.7032 Evaluate side-chains 157 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 121 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 631 PHE Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 344 HIS Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 654 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 99 optimal weight: 0.3980 chunk 85 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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: 0.6342 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7852 Z= 0.271 Angle : 0.703 9.811 10804 Z= 0.330 Chirality : 0.045 0.236 1378 Planarity : 0.005 0.058 1328 Dihedral : 9.483 89.763 1324 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 5.90 % Allowed : 25.56 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.27), residues: 1080 helix: 2.10 (0.21), residues: 622 sheet: None (None), residues: 0 loop : -1.73 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 501 HIS 0.001 0.000 HIS A 394 PHE 0.024 0.002 PHE B 591 TYR 0.008 0.001 TYR A 186 ARG 0.002 0.000 ARG B 252 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 121 time to evaluate : 0.712 Fit side-chains REVERT: A 137 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7639 (tp) REVERT: A 571 ILE cc_start: 0.7567 (mm) cc_final: 0.7262 (mt) REVERT: A 573 SER cc_start: 0.6641 (t) cc_final: 0.6338 (t) REVERT: A 654 TYR cc_start: 0.4928 (OUTLIER) cc_final: 0.3843 (t80) REVERT: B 137 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7662 (tp) REVERT: B 571 ILE cc_start: 0.7748 (mm) cc_final: 0.7496 (mt) REVERT: B 654 TYR cc_start: 0.4693 (OUTLIER) cc_final: 0.3608 (t80) outliers start: 42 outliers final: 34 residues processed: 159 average time/residue: 0.1443 time to fit residues: 33.7109 Evaluate side-chains 157 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 119 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 631 PHE Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 344 HIS Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 654 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 20.0000 chunk 85 optimal weight: 0.0470 chunk 35 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 75 optimal weight: 10.0000 overall best weight: 1.0282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.176455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.150231 restraints weight = 9774.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.153201 restraints weight = 5688.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.155513 restraints weight = 4110.245| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7852 Z= 0.273 Angle : 0.706 9.784 10804 Z= 0.333 Chirality : 0.045 0.241 1378 Planarity : 0.005 0.058 1328 Dihedral : 9.176 89.148 1324 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 6.46 % Allowed : 24.86 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.26), residues: 1080 helix: 2.11 (0.21), residues: 614 sheet: None (None), residues: 0 loop : -1.84 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 501 HIS 0.001 0.000 HIS A 394 PHE 0.026 0.002 PHE B 591 TYR 0.007 0.001 TYR A 186 ARG 0.002 0.000 ARG B 252 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1692.37 seconds wall clock time: 31 minutes 7.57 seconds (1867.57 seconds total)