Starting phenix.real_space_refine on Tue Nov 14 20:06:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dti_27699/11_2023/8dti_27699_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dti_27699/11_2023/8dti_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_27699/11_2023/8dti_27699.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dti_27699/11_2023/8dti_27699.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dti_27699/11_2023/8dti_27699_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dti_27699/11_2023/8dti_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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 5.27, per 1000 atoms: 0.56 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: 3.81 Conformation dependent library (CDL) restraints added in 1.7 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: 2.28 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: 2.71 Time building geometry restraints manager: 4.07 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: 5076 15.94 - 31.88: 450 31.88 - 47.82: 126 47.82 - 63.76: 18 63.76 - 79.70: 6 Dihedral angle restraints: 5676 sinusoidal: 1982 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 5673 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: 1.400 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: 0.000 Extract box with map and model: 7.430 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 28.380 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.020 ------------------------------------------------------------------------------- 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 : 13.313 79.702 3304 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 *********************** 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 : 1.096 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1545 time to fit residues: 30.0019 Evaluate side-chains 98 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.056 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3962 ------------------------------------------------------------------------------- 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: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9687 Z= 0.176 Angle : 0.478 7.028 13262 Z= 0.234 Chirality : 0.040 0.132 1523 Planarity : 0.003 0.027 1702 Dihedral : 3.997 40.548 1365 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.96 % Allowed : 8.15 % Favored : 90.89 % 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: 2.11 (0.25), residues: 1254 helix: 2.45 (0.19), residues: 792 sheet: 0.01 (0.49), residues: 122 loop : -0.63 (0.35), residues: 340 *********************** 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 117 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 108 time to evaluate : 1.141 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 114 average time/residue: 0.1498 time to fit residues: 27.2363 Evaluate side-chains 107 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 102 time to evaluate : 0.981 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0857 time to fit residues: 2.1501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN A 368 ASN A 467 HIS ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 ASN ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 9687 Z= 0.504 Angle : 0.710 7.681 13262 Z= 0.366 Chirality : 0.046 0.224 1523 Planarity : 0.005 0.053 1702 Dihedral : 4.757 42.706 1365 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.93 % Allowed : 13.29 % Favored : 84.78 % 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: 0.93 (0.24), residues: 1254 helix: 1.55 (0.18), residues: 792 sheet: -0.49 (0.52), residues: 102 loop : -1.13 (0.33), residues: 360 *********************** 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 111 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 93 time to evaluate : 1.089 Fit side-chains outliers start: 18 outliers final: 10 residues processed: 106 average time/residue: 0.1553 time to fit residues: 26.4693 Evaluate side-chains 99 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 1.016 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0874 time to fit residues: 3.1124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 0.0570 chunk 84 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 ASN ** B 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 661 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2309 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= 0.182 Angle : 0.510 6.716 13262 Z= 0.252 Chirality : 0.040 0.138 1523 Planarity : 0.004 0.039 1702 Dihedral : 4.269 38.927 1365 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.50 % Allowed : 13.93 % Favored : 84.57 % 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: 1.57 (0.25), residues: 1254 helix: 1.97 (0.19), residues: 806 sheet: -0.22 (0.50), residues: 114 loop : -0.76 (0.35), residues: 334 *********************** 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 115 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 101 time to evaluate : 1.148 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 112 average time/residue: 0.1527 time to fit residues: 27.8570 Evaluate side-chains 103 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 1.083 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0944 time to fit residues: 3.1513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 1 optimal weight: 2.9990 chunk 89 optimal weight: 0.0770 chunk 49 optimal weight: 0.0980 chunk 102 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2351 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= 0.169 Angle : 0.495 7.242 13262 Z= 0.244 Chirality : 0.039 0.118 1523 Planarity : 0.004 0.037 1702 Dihedral : 4.085 37.718 1365 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.18 % Allowed : 15.33 % Favored : 83.49 % 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: 1.75 (0.25), residues: 1254 helix: 2.11 (0.19), residues: 806 sheet: -0.16 (0.50), residues: 114 loop : -0.69 (0.35), residues: 334 *********************** 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 109 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 1.135 Fit side-chains outliers start: 11 outliers final: 3 residues processed: 108 average time/residue: 0.1570 time to fit residues: 27.2188 Evaluate side-chains 98 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 95 time to evaluate : 1.045 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0864 time to fit residues: 1.9150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0570 chunk 23 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 119 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9687 Z= 0.162 Angle : 0.496 7.474 13262 Z= 0.242 Chirality : 0.039 0.118 1523 Planarity : 0.004 0.035 1702 Dihedral : 4.005 36.775 1365 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.07 % Allowed : 16.29 % 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: 1.83 (0.25), residues: 1254 helix: 2.16 (0.19), residues: 806 sheet: -0.07 (0.51), residues: 114 loop : -0.66 (0.35), residues: 334 *********************** 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 108 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 1.123 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 106 average time/residue: 0.1588 time to fit residues: 26.7379 Evaluate side-chains 99 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 1.072 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0909 time to fit residues: 2.4455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 87 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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: 0.7733 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9687 Z= 0.203 Angle : 0.511 7.185 13262 Z= 0.251 Chirality : 0.039 0.121 1523 Planarity : 0.004 0.035 1702 Dihedral : 4.031 36.262 1365 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.07 % Allowed : 16.29 % 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: 1.75 (0.25), residues: 1254 helix: 2.11 (0.19), residues: 806 sheet: -0.16 (0.51), residues: 114 loop : -0.71 (0.35), residues: 334 *********************** 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 108 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 1.209 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 106 average time/residue: 0.1580 time to fit residues: 26.8563 Evaluate side-chains 98 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 92 time to evaluate : 1.113 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0889 time to fit residues: 2.2865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 75 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 93 optimal weight: 0.1980 chunk 108 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9687 Z= 0.160 Angle : 0.504 8.153 13262 Z= 0.244 Chirality : 0.039 0.123 1523 Planarity : 0.003 0.034 1702 Dihedral : 3.959 35.354 1365 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.54 % Allowed : 16.93 % Favored : 82.53 % 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: 1.87 (0.25), residues: 1254 helix: 2.20 (0.19), residues: 806 sheet: -0.18 (0.51), residues: 114 loop : -0.63 (0.35), residues: 334 *********************** 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 101 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 1.321 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 100 average time/residue: 0.1687 time to fit residues: 26.9551 Evaluate side-chains 95 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 1.080 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0846 time to fit residues: 1.4346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 111 optimal weight: 0.3980 chunk 67 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 100 optimal weight: 0.3980 chunk 105 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9687 Z= 0.173 Angle : 0.511 7.123 13262 Z= 0.248 Chirality : 0.039 0.157 1523 Planarity : 0.003 0.033 1702 Dihedral : 3.939 35.329 1365 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.54 % Allowed : 18.01 % Favored : 81.46 % 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: 1.85 (0.25), residues: 1254 helix: 2.20 (0.19), residues: 806 sheet: -0.18 (0.50), residues: 114 loop : -0.66 (0.35), residues: 334 *********************** 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 102 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 97 time to evaluate : 1.197 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 101 average time/residue: 0.1667 time to fit residues: 26.8605 Evaluate side-chains 96 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 94 time to evaluate : 1.143 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0875 time to fit residues: 1.7069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 123 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 98 optimal weight: 0.0980 chunk 10 optimal weight: 0.2980 chunk 75 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9687 Z= 0.173 Angle : 0.536 10.568 13262 Z= 0.255 Chirality : 0.040 0.291 1523 Planarity : 0.003 0.033 1702 Dihedral : 3.936 35.145 1365 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.11 % Allowed : 18.54 % Favored : 81.35 % 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: 1.80 (0.25), residues: 1254 helix: 2.13 (0.19), residues: 808 sheet: -0.15 (0.51), residues: 114 loop : -0.65 (0.35), residues: 332 ********************** 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 97 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 1.100 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 97 average time/residue: 0.1620 time to fit residues: 25.0764 Evaluate side-chains 95 residues out of total 1074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 1.000 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 0.1980 chunk 14 optimal weight: 0.0670 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 12 optimal weight: 0.3980 chunk 18 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.115543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.097454 restraints weight = 21577.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.100390 restraints weight = 13440.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.102427 restraints weight = 9568.667| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9687 Z= 0.150 Angle : 0.516 9.512 13262 Z= 0.247 Chirality : 0.040 0.268 1523 Planarity : 0.003 0.034 1702 Dihedral : 3.881 34.728 1365 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.43 % Allowed : 18.33 % 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: 2.19 (0.19), residues: 808 sheet: -0.09 (0.51), residues: 114 loop : -0.60 (0.35), residues: 332 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1802.90 seconds wall clock time: 33 minutes 51.12 seconds (2031.12 seconds total)