Starting phenix.real_space_refine on Thu Mar 14 18:39:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dti_27699/03_2024/8dti_27699_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dti_27699/03_2024/8dti_27699.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dti_27699/03_2024/8dti_27699.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dti_27699/03_2024/8dti_27699.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dti_27699/03_2024/8dti_27699_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dti_27699/03_2024/8dti_27699_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.976 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 63 5.16 5 C 6018 2.51 5 N 1594 2.21 5 O 1776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9455 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 4684 Classifications: {'peptide': 629} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 598} Unresolved non-hydrogen bonds: 268 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 226 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'TYR:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 134 Chain: "B" Number of atoms: 4695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 4695 Classifications: {'peptide': 629} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 598} Unresolved non-hydrogen bonds: 257 Unresolved non-hydrogen angles: 309 Unresolved non-hydrogen dihedrals: 216 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'TYR:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 125 Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Classifications: {'RNA': 1} Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Classifications: {'RNA': 1} Time building chain proxies: 5.77, per 1000 atoms: 0.61 Number of scatterers: 9455 At special positions: 0 Unit cell: (156.6, 78.84, 78.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 63 16.00 P 4 15.00 O 1776 8.00 N 1594 7.00 C 6018 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.88 Conformation dependent library (CDL) restraints added in 1.8 seconds 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2372 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 8 sheets defined 57.7% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.13 Creating SS restraints... Processing helix chain 'A' and resid 220 through 233 Processing helix chain 'A' and resid 236 through 249 Processing helix chain 'A' and resid 254 through 274 Processing helix chain 'A' and resid 277 through 290 Processing helix chain 'A' and resid 295 through 307 Processing helix chain 'A' and resid 311 through 324 Processing helix chain 'A' and resid 329 through 342 Processing helix chain 'A' and resid 345 through 358 Processing helix chain 'A' and resid 363 through 376 Processing helix chain 'A' and resid 379 through 392 Processing helix chain 'A' and resid 397 through 410 Processing helix chain 'A' and resid 414 through 426 Processing helix chain 'A' and resid 431 through 444 removed outlier: 3.616A pdb=" N TYR A 443 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE A 444 " --> pdb=" O ALA A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 466 Processing helix chain 'A' and resid 496 through 507 removed outlier: 4.323A pdb=" N ALA A 503 " --> pdb=" O TYR A 499 " (cutoff:3.500A) Proline residue: A 504 - end of helix Processing helix chain 'A' and resid 526 through 538 Processing helix chain 'A' and resid 550 through 560 Processing helix chain 'A' and resid 577 through 580 No H-bonds generated for 'chain 'A' and resid 577 through 580' Processing helix chain 'A' and resid 649 through 652 No H-bonds generated for 'chain 'A' and resid 649 through 652' Processing helix chain 'A' and resid 663 through 665 No H-bonds generated for 'chain 'A' and resid 663 through 665' Processing helix chain 'A' and resid 668 through 680 Processing helix chain 'A' and resid 696 through 709 Processing helix chain 'A' and resid 713 through 715 No H-bonds generated for 'chain 'A' and resid 713 through 715' Processing helix chain 'A' and resid 725 through 734 removed outlier: 4.183A pdb=" N TYR A 732 " --> pdb=" O HIS A 728 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N SER A 733 " --> pdb=" O MET A 729 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LEU A 734 " --> pdb=" O GLN A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 756 Processing helix chain 'A' and resid 768 through 780 removed outlier: 4.728A pdb=" N GLY A 773 " --> pdb=" O ALA A 769 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N VAL A 774 " --> pdb=" O HIS A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 785 No H-bonds generated for 'chain 'A' and resid 783 through 785' Processing helix chain 'A' and resid 790 through 802 Processing helix chain 'A' and resid 805 through 819 removed outlier: 4.203A pdb=" N ARG A 815 " --> pdb=" O ARG A 811 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ASP A 816 " --> pdb=" O MET A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 845 Processing helix chain 'B' and resid 220 through 233 Processing helix chain 'B' and resid 236 through 249 Processing helix chain 'B' and resid 254 through 274 Processing helix chain 'B' and resid 277 through 290 Processing helix chain 'B' and resid 295 through 307 Processing helix chain 'B' and resid 311 through 324 Processing helix chain 'B' and resid 329 through 342 Processing helix chain 'B' and resid 345 through 358 Processing helix chain 'B' and resid 363 through 376 Processing helix chain 'B' and resid 379 through 392 Processing helix chain 'B' and resid 397 through 410 Processing helix chain 'B' and resid 414 through 426 Processing helix chain 'B' and resid 431 through 444 removed outlier: 3.616A pdb=" N TYR B 443 " --> pdb=" O LEU B 439 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE B 444 " --> pdb=" O ALA B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 466 Processing helix chain 'B' and resid 496 through 507 removed outlier: 4.323A pdb=" N ALA B 503 " --> pdb=" O TYR B 499 " (cutoff:3.500A) Proline residue: B 504 - end of helix Processing helix chain 'B' and resid 526 through 538 Processing helix chain 'B' and resid 550 through 560 Processing helix chain 'B' and resid 577 through 580 No H-bonds generated for 'chain 'B' and resid 577 through 580' Processing helix chain 'B' and resid 649 through 652 No H-bonds generated for 'chain 'B' and resid 649 through 652' Processing helix chain 'B' and resid 663 through 665 No H-bonds generated for 'chain 'B' and resid 663 through 665' Processing helix chain 'B' and resid 668 through 680 Processing helix chain 'B' and resid 696 through 709 Processing helix chain 'B' and resid 713 through 715 No H-bonds generated for 'chain 'B' and resid 713 through 715' Processing helix chain 'B' and resid 725 through 734 removed outlier: 4.184A pdb=" N TYR B 732 " --> pdb=" O HIS B 728 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N SER B 733 " --> pdb=" O MET B 729 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LEU B 734 " --> pdb=" O GLN B 730 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 756 Processing helix chain 'B' and resid 768 through 780 removed outlier: 4.729A pdb=" N GLY B 773 " --> pdb=" O ALA B 769 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N VAL B 774 " --> pdb=" O HIS B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 785 No H-bonds generated for 'chain 'B' and resid 783 through 785' Processing helix chain 'B' and resid 790 through 802 Processing helix chain 'B' and resid 805 through 819 removed outlier: 4.203A pdb=" N ARG B 815 " --> pdb=" O ARG B 811 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ASP B 816 " --> pdb=" O MET B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 845 Processing sheet with id= A, first strand: chain 'A' and resid 587 through 590 removed outlier: 6.895A pdb=" N VAL A 541 " --> pdb=" O VAL A 517 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N SER A 519 " --> pdb=" O VAL A 541 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LYS A 543 " --> pdb=" O SER A 519 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 605 through 609 removed outlier: 6.594A pdb=" N GLU A 624 " --> pdb=" O ARG A 606 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N THR A 608 " --> pdb=" O GLU A 624 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N VAL A 626 " --> pdb=" O THR A 608 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 655 through 659 Processing sheet with id= D, first strand: chain 'A' and resid 737 through 739 No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 587 through 590 removed outlier: 6.894A pdb=" N VAL B 541 " --> pdb=" O VAL B 517 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N SER B 519 " --> pdb=" O VAL B 541 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LYS B 543 " --> pdb=" O SER B 519 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 605 through 609 removed outlier: 6.594A pdb=" N GLU B 624 " --> pdb=" O ARG B 606 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N THR B 608 " --> pdb=" O GLU B 624 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N VAL B 626 " --> pdb=" O THR B 608 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 655 through 659 Processing sheet with id= H, first strand: chain 'B' and resid 737 through 739 No H-bonds generated for sheet with id= H 508 hydrogen bonds defined for protein. 1518 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: 2.96 Time building geometry restraints manager: 4.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1952 1.33 - 1.45: 2285 1.45 - 1.57: 5347 1.57 - 1.69: 8 1.69 - 1.81: 95 Bond restraints: 9687 Sorted by residual: bond pdb=" C4 GFB A1001 " pdb=" N3 GFB A1001 " ideal model delta sigma weight residual 1.340 1.503 -0.163 2.00e-02 2.50e+03 6.65e+01 bond pdb=" C4 GFB B1001 " pdb=" N3 GFB B1001 " ideal model delta sigma weight residual 1.340 1.503 -0.163 2.00e-02 2.50e+03 6.63e+01 bond pdb=" C2 GFB A1001 " pdb=" N2 GFB A1001 " ideal model delta sigma weight residual 1.341 1.491 -0.150 2.00e-02 2.50e+03 5.61e+01 bond pdb=" C2 GFB B1001 " pdb=" N2 GFB B1001 " ideal model delta sigma weight residual 1.341 1.490 -0.149 2.00e-02 2.50e+03 5.57e+01 bond pdb=" C2 GFB B1001 " pdb=" N3 GFB B1001 " ideal model delta sigma weight residual 1.310 1.451 -0.141 2.00e-02 2.50e+03 4.98e+01 ... (remaining 9682 not shown) Histogram of bond angle deviations from ideal: 99.72 - 106.57: 308 106.57 - 113.43: 5293 113.43 - 120.28: 3497 120.28 - 127.13: 4035 127.13 - 133.98: 129 Bond angle restraints: 13262 Sorted by residual: angle pdb=" O2P GFB B1001 " pdb=" P GFB B1001 " pdb=" O5' GFB B1001 " ideal model delta sigma weight residual 93.35 108.86 -15.51 3.00e+00 1.11e-01 2.67e+01 angle pdb=" O2P GFB A1001 " pdb=" P GFB A1001 " pdb=" O5' GFB A1001 " ideal model delta sigma weight residual 93.35 108.84 -15.49 3.00e+00 1.11e-01 2.66e+01 angle pdb=" O1X GFB A1001 " pdb=" P1 GFB A1001 " pdb=" O2X GFB A1001 " ideal model delta sigma weight residual 122.73 109.50 13.23 3.00e+00 1.11e-01 1.94e+01 angle pdb=" O1X GFB B1001 " pdb=" P1 GFB B1001 " pdb=" O2X GFB B1001 " ideal model delta sigma weight residual 122.73 109.55 13.18 3.00e+00 1.11e-01 1.93e+01 angle pdb=" O1 GFB A1001 " pdb=" P1 GFB A1001 " pdb=" O2P GFB A1001 " ideal model delta sigma weight residual 99.26 109.54 -10.28 3.00e+00 1.11e-01 1.17e+01 ... (remaining 13257 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.94: 5124 15.94 - 31.88: 460 31.88 - 47.82: 142 47.82 - 63.76: 34 63.76 - 79.70: 16 Dihedral angle restraints: 5776 sinusoidal: 2082 harmonic: 3694 Sorted by residual: dihedral pdb=" CG ARG A 532 " pdb=" CD ARG A 532 " pdb=" NE ARG A 532 " pdb=" CZ ARG A 532 " ideal model delta sinusoidal sigma weight residual -180.00 -137.41 -42.59 2 1.50e+01 4.44e-03 9.77e+00 dihedral pdb=" CG ARG B 532 " pdb=" CD ARG B 532 " pdb=" NE ARG B 532 " pdb=" CZ ARG B 532 " ideal model delta sinusoidal sigma weight residual -180.00 -137.46 -42.54 2 1.50e+01 4.44e-03 9.75e+00 dihedral pdb=" CB MET B 441 " pdb=" CG MET B 441 " pdb=" SD MET B 441 " pdb=" CE MET B 441 " ideal model delta sinusoidal sigma weight residual -180.00 -120.28 -59.72 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 5773 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1368 0.070 - 0.140: 149 0.140 - 0.209: 4 0.209 - 0.279: 0 0.279 - 0.349: 2 Chirality restraints: 1523 Sorted by residual: chirality pdb=" C2' GFB B1001 " pdb=" C1' GFB B1001 " pdb=" C3' GFB B1001 " pdb=" O2' GFB B1001 " both_signs ideal model delta sigma weight residual False -2.56 -2.91 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" C2' GFB A1001 " pdb=" C1' GFB A1001 " pdb=" C3' GFB A1001 " pdb=" O2' GFB A1001 " both_signs ideal model delta sigma weight residual False -2.56 -2.90 0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" C5A GFB B1001 " pdb=" C4A GFB B1001 " pdb=" C6A GFB B1001 " pdb=" O5 GFB B1001 " both_signs ideal model delta sigma weight residual False 2.42 2.63 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1520 not shown) Planarity restraints: 1702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 420 " 0.022 2.00e-02 2.50e+03 1.87e-02 7.02e+00 pdb=" CG TYR B 420 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR B 420 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR B 420 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR B 420 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 420 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 420 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 420 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 420 " -0.022 2.00e-02 2.50e+03 1.87e-02 6.97e+00 pdb=" CG TYR A 420 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR A 420 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 420 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR A 420 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 420 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 420 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 420 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 420 " 0.007 2.00e-02 2.50e+03 1.35e-02 1.83e+00 pdb=" C TYR B 420 " -0.023 2.00e-02 2.50e+03 pdb=" O TYR B 420 " 0.009 2.00e-02 2.50e+03 pdb=" N GLU B 421 " 0.008 2.00e-02 2.50e+03 ... (remaining 1699 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 741 2.74 - 3.28: 10049 3.28 - 3.82: 16302 3.82 - 4.36: 18012 4.36 - 4.90: 30524 Nonbonded interactions: 75628 Sorted by model distance: nonbonded pdb=" OG1 THR A 748 " pdb=" OE2 GLU A 752 " model vdw 2.196 2.440 nonbonded pdb=" OG1 THR B 748 " pdb=" OE2 GLU B 752 " model vdw 2.196 2.440 nonbonded pdb=" OH TYR B 518 " pdb=" OD2 ASP B 560 " model vdw 2.213 2.440 nonbonded pdb=" OH TYR A 518 " pdb=" OD2 ASP A 560 " model vdw 2.214 2.440 nonbonded pdb=" O LEU A 505 " pdb=" OH TYR A 510 " model vdw 2.231 2.440 ... (remaining 75623 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 218 through 226 and (name N or name CA or name C or name \ O or name CB )) or resid 227 or (resid 228 through 231 and (name N or name CA or \ name C or name O or name CB )) or resid 232 through 846 or resid 1001)) selection = (chain 'B' and (resid 218 through 232 or (resid 233 and (name N or name CA or na \ me C or name O or name CB )) or resid 234 through 236 or (resid 237 through 239 \ and (name N or name CA or name C or name O or name CB )) or resid 240 through 77 \ 8 or (resid 779 and (name N or name CA or name C or name O or name CB )) or resi \ d 780 through 846 or resid 1001)) } 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: 1.480 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: 7.420 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 29.900 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.163 9687 Z= 0.448 Angle : 0.659 15.513 13262 Z= 0.306 Chirality : 0.041 0.349 1523 Planarity : 0.003 0.032 1702 Dihedral : 14.507 79.702 3404 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.82 (0.25), residues: 1254 helix: 2.19 (0.19), residues: 778 sheet: 0.11 (0.49), residues: 122 loop : -0.63 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 459 HIS 0.003 0.001 HIS B 508 PHE 0.018 0.001 PHE A 724 TYR 0.045 0.001 TYR B 420 ARG 0.002 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.070 Fit side-chains REVERT: A 632 PHE cc_start: 0.6534 (p90) cc_final: 0.6318 (p90) REVERT: B 632 PHE cc_start: 0.7292 (p90) cc_final: 0.7026 (p90) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1526 time to fit residues: 29.5609 Evaluate side-chains 98 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 37 optimal weight: 0.0970 chunk 59 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 112 optimal weight: 2.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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: 0.7609 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9687 Z= 0.175 Angle : 0.480 7.144 13262 Z= 0.234 Chirality : 0.040 0.127 1523 Planarity : 0.003 0.026 1702 Dihedral : 7.647 73.993 1465 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.96 % Allowed : 7.72 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.25), residues: 1254 helix: 2.45 (0.19), residues: 792 sheet: 0.01 (0.49), residues: 122 loop : -0.65 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 473 HIS 0.008 0.001 HIS A 467 PHE 0.018 0.002 PHE B 500 TYR 0.025 0.001 TYR B 420 ARG 0.002 0.000 ARG A 811 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 109 time to evaluate : 1.195 Fit side-chains REVERT: A 318 TYR cc_start: 0.8533 (m-80) cc_final: 0.7815 (m-80) REVERT: A 406 LEU cc_start: 0.8364 (tt) cc_final: 0.8123 (mt) REVERT: B 290 TYR cc_start: 0.8675 (m-80) cc_final: 0.8426 (m-80) REVERT: B 508 HIS cc_start: 0.7557 (OUTLIER) cc_final: 0.7236 (t-90) REVERT: B 632 PHE cc_start: 0.7638 (p90) cc_final: 0.7055 (p90) outliers start: 9 outliers final: 6 residues processed: 115 average time/residue: 0.1477 time to fit residues: 27.0618 Evaluate side-chains 109 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 102 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 508 HIS Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 724 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 111 optimal weight: 0.3980 chunk 38 optimal weight: 0.0060 chunk 90 optimal weight: 0.0170 overall best weight: 0.8036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN A 661 ASN B 368 ASN B 661 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9687 Z= 0.192 Angle : 0.480 7.023 13262 Z= 0.237 Chirality : 0.039 0.120 1523 Planarity : 0.003 0.029 1702 Dihedral : 6.414 74.910 1465 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.39 % Allowed : 11.68 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.25), residues: 1254 helix: 2.46 (0.19), residues: 794 sheet: -0.27 (0.49), residues: 122 loop : -0.53 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 459 HIS 0.010 0.001 HIS A 467 PHE 0.019 0.002 PHE A 724 TYR 0.019 0.001 TYR B 299 ARG 0.003 0.000 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 1.167 Fit side-chains REVERT: A 318 TYR cc_start: 0.8440 (m-80) cc_final: 0.7753 (m-80) REVERT: A 729 MET cc_start: 0.8089 (tpp) cc_final: 0.7867 (tpp) REVERT: B 290 TYR cc_start: 0.8702 (m-80) cc_final: 0.8449 (m-80) REVERT: B 508 HIS cc_start: 0.7788 (OUTLIER) cc_final: 0.7255 (t-90) REVERT: B 632 PHE cc_start: 0.7533 (p90) cc_final: 0.6960 (p90) outliers start: 13 outliers final: 7 residues processed: 113 average time/residue: 0.1558 time to fit residues: 28.2200 Evaluate side-chains 105 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 97 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 508 HIS Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 814 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 12 optimal weight: 0.2980 chunk 53 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 119 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 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 467 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9687 Z= 0.170 Angle : 0.471 7.319 13262 Z= 0.229 Chirality : 0.039 0.123 1523 Planarity : 0.003 0.029 1702 Dihedral : 6.456 79.399 1465 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.39 % Allowed : 12.75 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.25), residues: 1254 helix: 2.40 (0.19), residues: 806 sheet: -0.19 (0.55), residues: 102 loop : -0.49 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 459 HIS 0.007 0.001 HIS A 467 PHE 0.018 0.002 PHE A 724 TYR 0.016 0.001 TYR B 793 ARG 0.002 0.000 ARG A 815 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 104 time to evaluate : 1.005 Fit side-chains REVERT: A 318 TYR cc_start: 0.8411 (m-80) cc_final: 0.7674 (m-80) REVERT: A 491 ASP cc_start: 0.7590 (OUTLIER) cc_final: 0.7149 (p0) REVERT: A 756 MET cc_start: 0.7853 (mmp) cc_final: 0.7611 (mmm) REVERT: B 290 TYR cc_start: 0.8690 (m-80) cc_final: 0.8444 (m-80) REVERT: B 343 ASP cc_start: 0.7148 (t70) cc_final: 0.6901 (t70) REVERT: B 508 HIS cc_start: 0.7742 (OUTLIER) cc_final: 0.7263 (t-90) REVERT: B 632 PHE cc_start: 0.7522 (p90) cc_final: 0.6991 (p90) outliers start: 13 outliers final: 10 residues processed: 115 average time/residue: 0.1542 time to fit residues: 28.5031 Evaluate side-chains 105 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 508 HIS Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 508 HIS Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 814 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9687 Z= 0.223 Angle : 0.496 7.127 13262 Z= 0.245 Chirality : 0.039 0.118 1523 Planarity : 0.003 0.031 1702 Dihedral : 6.524 77.634 1465 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.57 % Allowed : 13.50 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.99 (0.25), residues: 1254 helix: 2.33 (0.19), residues: 804 sheet: -0.22 (0.54), residues: 102 loop : -0.62 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 459 HIS 0.004 0.001 HIS B 508 PHE 0.019 0.002 PHE A 724 TYR 0.019 0.001 TYR A 420 ARG 0.002 0.000 ARG A 811 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 99 time to evaluate : 1.101 Fit side-chains REVERT: A 318 TYR cc_start: 0.8366 (m-80) cc_final: 0.7705 (m-80) REVERT: A 491 ASP cc_start: 0.7759 (OUTLIER) cc_final: 0.7056 (p0) REVERT: B 290 TYR cc_start: 0.8733 (m-80) cc_final: 0.8477 (m-80) REVERT: B 343 ASP cc_start: 0.7230 (t70) cc_final: 0.6956 (t70) REVERT: B 491 ASP cc_start: 0.7996 (OUTLIER) cc_final: 0.7296 (p0) REVERT: B 508 HIS cc_start: 0.7722 (OUTLIER) cc_final: 0.7154 (t-90) REVERT: B 556 MET cc_start: 0.7815 (ppp) cc_final: 0.7346 (ppp) REVERT: B 632 PHE cc_start: 0.7504 (p90) cc_final: 0.6920 (p90) outliers start: 24 outliers final: 16 residues processed: 119 average time/residue: 0.1441 time to fit residues: 27.5584 Evaluate side-chains 114 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 95 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 508 HIS Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 508 HIS Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 814 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 ASN A 402 ASN ** B 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9687 Z= 0.200 Angle : 0.496 8.584 13262 Z= 0.242 Chirality : 0.039 0.118 1523 Planarity : 0.003 0.032 1702 Dihedral : 6.486 75.522 1465 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.68 % Allowed : 14.68 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.90 (0.25), residues: 1254 helix: 2.36 (0.19), residues: 794 sheet: -0.52 (0.49), residues: 122 loop : -0.73 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 459 HIS 0.004 0.001 HIS B 508 PHE 0.019 0.002 PHE A 724 TYR 0.020 0.001 TYR B 420 ARG 0.002 0.000 ARG A 811 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 95 time to evaluate : 1.122 Fit side-chains REVERT: A 232 ASN cc_start: 0.7378 (m-40) cc_final: 0.7075 (p0) REVERT: A 318 TYR cc_start: 0.8395 (m-80) cc_final: 0.7733 (m-80) REVERT: A 491 ASP cc_start: 0.7827 (OUTLIER) cc_final: 0.7116 (p0) REVERT: B 290 TYR cc_start: 0.8719 (m-80) cc_final: 0.8475 (m-80) REVERT: B 343 ASP cc_start: 0.7270 (t70) cc_final: 0.6982 (t70) REVERT: B 491 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7280 (p0) REVERT: B 508 HIS cc_start: 0.7702 (OUTLIER) cc_final: 0.7182 (t-90) REVERT: B 632 PHE cc_start: 0.7596 (p90) cc_final: 0.6958 (p90) outliers start: 25 outliers final: 17 residues processed: 118 average time/residue: 0.1536 time to fit residues: 28.7786 Evaluate side-chains 112 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 92 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 508 HIS Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 508 HIS Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 814 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 119 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9687 Z= 0.228 Angle : 0.524 7.719 13262 Z= 0.257 Chirality : 0.040 0.140 1523 Planarity : 0.004 0.033 1702 Dihedral : 6.547 74.115 1465 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.00 % Allowed : 15.11 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.72 (0.25), residues: 1254 helix: 2.22 (0.19), residues: 796 sheet: -1.21 (0.52), residues: 102 loop : -0.62 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 459 HIS 0.004 0.001 HIS B 508 PHE 0.021 0.002 PHE A 724 TYR 0.022 0.002 TYR A 420 ARG 0.002 0.000 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 92 time to evaluate : 1.055 Fit side-chains REVERT: A 318 TYR cc_start: 0.8377 (m-80) cc_final: 0.7757 (m-80) REVERT: A 491 ASP cc_start: 0.7865 (OUTLIER) cc_final: 0.7114 (p0) REVERT: B 343 ASP cc_start: 0.7567 (t70) cc_final: 0.7268 (t70) REVERT: B 491 ASP cc_start: 0.7934 (OUTLIER) cc_final: 0.7094 (p0) REVERT: B 508 HIS cc_start: 0.7741 (OUTLIER) cc_final: 0.7204 (t-90) REVERT: B 632 PHE cc_start: 0.7655 (p90) cc_final: 0.6874 (p90) outliers start: 28 outliers final: 22 residues processed: 116 average time/residue: 0.1471 time to fit residues: 27.6403 Evaluate side-chains 115 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 90 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 508 HIS Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 508 HIS Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 814 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 23 optimal weight: 0.0980 chunk 75 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 93 optimal weight: 0.5980 chunk 108 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9687 Z= 0.159 Angle : 0.500 8.487 13262 Z= 0.241 Chirality : 0.039 0.119 1523 Planarity : 0.003 0.032 1702 Dihedral : 6.321 70.246 1465 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.89 % Allowed : 15.86 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.89 (0.25), residues: 1254 helix: 2.24 (0.19), residues: 806 sheet: -0.72 (0.55), residues: 94 loop : -0.49 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 461 HIS 0.003 0.001 HIS B 508 PHE 0.021 0.001 PHE A 724 TYR 0.026 0.001 TYR B 318 ARG 0.001 0.000 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 97 time to evaluate : 1.243 Fit side-chains revert: symmetry clash REVERT: A 232 ASN cc_start: 0.6305 (p0) cc_final: 0.6039 (p0) REVERT: A 318 TYR cc_start: 0.8372 (m-80) cc_final: 0.7773 (m-80) REVERT: A 491 ASP cc_start: 0.7844 (OUTLIER) cc_final: 0.7113 (p0) REVERT: B 290 TYR cc_start: 0.8702 (m-80) cc_final: 0.8481 (m-80) REVERT: B 343 ASP cc_start: 0.7545 (t70) cc_final: 0.7262 (t70) REVERT: B 491 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7050 (p0) REVERT: B 508 HIS cc_start: 0.7698 (OUTLIER) cc_final: 0.7330 (t-90) REVERT: B 632 PHE cc_start: 0.7600 (p90) cc_final: 0.6787 (p90) outliers start: 27 outliers final: 23 residues processed: 120 average time/residue: 0.1581 time to fit residues: 29.8208 Evaluate side-chains 119 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 93 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 508 HIS Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 508 HIS Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 814 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.8980 chunk 104 optimal weight: 0.5980 chunk 111 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9687 Z= 0.197 Angle : 0.513 7.487 13262 Z= 0.249 Chirality : 0.039 0.123 1523 Planarity : 0.003 0.032 1702 Dihedral : 6.307 69.554 1465 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.89 % Allowed : 15.97 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.74 (0.25), residues: 1254 helix: 2.24 (0.19), residues: 796 sheet: -1.18 (0.52), residues: 102 loop : -0.61 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 461 HIS 0.004 0.001 HIS B 508 PHE 0.021 0.002 PHE A 724 TYR 0.019 0.001 TYR A 299 ARG 0.002 0.000 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 94 time to evaluate : 1.137 Fit side-chains revert: symmetry clash REVERT: A 232 ASN cc_start: 0.6212 (p0) cc_final: 0.5942 (p0) REVERT: A 308 MET cc_start: 0.6988 (ptt) cc_final: 0.6774 (ptp) REVERT: A 318 TYR cc_start: 0.8369 (m-80) cc_final: 0.7775 (m-80) REVERT: A 491 ASP cc_start: 0.7887 (OUTLIER) cc_final: 0.7146 (p0) REVERT: B 343 ASP cc_start: 0.7576 (t70) cc_final: 0.7288 (t70) REVERT: B 491 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7032 (p0) REVERT: B 508 HIS cc_start: 0.7708 (OUTLIER) cc_final: 0.7278 (t-90) REVERT: B 632 PHE cc_start: 0.7515 (p90) cc_final: 0.6698 (p90) outliers start: 27 outliers final: 23 residues processed: 117 average time/residue: 0.1528 time to fit residues: 28.3542 Evaluate side-chains 118 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 92 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 508 HIS Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 508 HIS Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 814 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 3.9990 chunk 71 optimal weight: 0.0980 chunk 55 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 123 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 98 optimal weight: 0.3980 chunk 10 optimal weight: 0.0870 chunk 75 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9687 Z= 0.142 Angle : 0.490 7.350 13262 Z= 0.236 Chirality : 0.039 0.118 1523 Planarity : 0.003 0.032 1702 Dihedral : 6.074 65.285 1465 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.47 % Allowed : 16.29 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.98 (0.25), residues: 1254 helix: 2.28 (0.19), residues: 806 sheet: -0.10 (0.51), residues: 114 loop : -0.57 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 461 HIS 0.002 0.001 HIS B 456 PHE 0.022 0.001 PHE A 724 TYR 0.026 0.001 TYR B 318 ARG 0.001 0.000 ARG A 815 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 96 time to evaluate : 1.127 Fit side-chains REVERT: A 232 ASN cc_start: 0.6207 (p0) cc_final: 0.5940 (p0) REVERT: A 308 MET cc_start: 0.6935 (ptt) cc_final: 0.6718 (ptp) REVERT: A 318 TYR cc_start: 0.8360 (m-80) cc_final: 0.7759 (m-80) REVERT: A 491 ASP cc_start: 0.7763 (OUTLIER) cc_final: 0.7054 (p0) REVERT: B 491 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7039 (p0) REVERT: B 632 PHE cc_start: 0.7462 (p90) cc_final: 0.6647 (p90) outliers start: 23 outliers final: 20 residues processed: 115 average time/residue: 0.1540 time to fit residues: 28.1496 Evaluate side-chains 115 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 93 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 814 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.0370 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 0.0980 chunk 14 optimal weight: 0.2980 chunk 27 optimal weight: 3.9990 chunk 98 optimal weight: 0.0770 chunk 41 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 overall best weight: 0.2216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 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 = 0.3693 r_free = 0.3693 target = 0.116945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.099329 restraints weight = 21316.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.102231 restraints weight = 13326.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.104200 restraints weight = 9420.941| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9687 Z= 0.127 Angle : 0.485 7.813 13262 Z= 0.233 Chirality : 0.038 0.116 1523 Planarity : 0.003 0.031 1702 Dihedral : 5.849 62.081 1465 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.36 % Allowed : 17.36 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.25), residues: 1254 helix: 2.38 (0.19), residues: 806 sheet: -0.06 (0.52), residues: 114 loop : -0.54 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 461 HIS 0.003 0.001 HIS B 456 PHE 0.023 0.001 PHE A 724 TYR 0.022 0.001 TYR A 299 ARG 0.002 0.000 ARG B 342 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1818.76 seconds wall clock time: 33 minutes 45.24 seconds (2025.24 seconds total)