Starting phenix.real_space_refine (version: 1.21rc1) on Wed Oct 4 15:59:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v07_26940/10_2023/7v07_26940_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v07_26940/10_2023/7v07_26940.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v07_26940/10_2023/7v07_26940_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v07_26940/10_2023/7v07_26940_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v07_26940/10_2023/7v07_26940_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v07_26940/10_2023/7v07_26940.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v07_26940/10_2023/7v07_26940.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v07_26940/10_2023/7v07_26940_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v07_26940/10_2023/7v07_26940_updated.pdb" } resolution = 2.8 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= 0.001 sd= 0.162 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 8 5.49 5 S 38 5.16 5 C 6134 2.51 5 N 1410 2.21 5 O 1572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 89": "OE1" <-> "OE2" Residue "D TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 473": "OE1" <-> "OE2" Residue "C GLU 480": "OE1" <-> "OE2" Residue "C PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 535": "OE1" <-> "OE2" Residue "C PHE 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 621": "OD1" <-> "OD2" Residue "C PHE 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 755": "OE1" <-> "OE2" Residue "C TYR 794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 889": "OD1" <-> "OD2" Residue "E ASP 385": "OD1" <-> "OD2" Residue "E ASP 396": "OD1" <-> "OD2" Residue "E PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 439": "OE1" <-> "OE2" Residue "E PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 485": "OE1" <-> "OE2" Residue "E PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 522": "OE1" <-> "OE2" Residue "E GLU 535": "OE1" <-> "OE2" Residue "E ASP 546": "OD1" <-> "OD2" Residue "E TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 621": "OD1" <-> "OD2" Residue "E GLU 681": "OE1" <-> "OE2" Residue "E GLU 882": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 9162 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 302 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 38} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 302 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 38} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 4063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4063 Classifications: {'peptide': 517} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 488} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 4063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4063 Classifications: {'peptide': 517} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 488} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "F" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 98 Unusual residues: {'CLR': 2, 'PLC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 192 Unusual residues: {'CLR': 2, 'PIO': 2, 'PLC': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 5.60, per 1000 atoms: 0.61 Number of scatterers: 9162 At special positions: 0 Unit cell: (142.345, 86.735, 115.785, 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 38 16.00 P 8 15.00 O 1572 8.00 N 1410 7.00 C 6134 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA A 3 " - " MAN A 4 " " BMA F 3 " - " MAN F 4 " ALPHA1-4 " BMA A 3 " - " MAN A 5 " " BMA F 3 " - " MAN F 5 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " BETA1-6 " NAG A 1 " - " FUC A 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG F 1 " - " FUC F 6 " NAG-ASN " NAG A 1 " - " ASN C 642 " " NAG F 1 " - " ASN E 642 " Time building additional restraints: 4.37 Conformation dependent library (CDL) restraints added in 1.4 seconds 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2064 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 2 sheets defined 66.5% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'B' and resid 89 through 113 Processing helix chain 'D' and resid 89 through 113 Processing helix chain 'C' and resid 380 through 393 removed outlier: 3.536A pdb=" N ARG C 389 " --> pdb=" O ASP C 385 " (cutoff:3.500A) Proline residue: C 391 - end of helix Processing helix chain 'C' and resid 395 through 400 removed outlier: 5.133A pdb=" N ALA C 400 " --> pdb=" O ASP C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 431 removed outlier: 3.636A pdb=" N PHE C 414 " --> pdb=" O ILE C 410 " (cutoff:3.500A) Proline residue: C 419 - end of helix Processing helix chain 'C' and resid 437 through 454 Processing helix chain 'C' and resid 466 through 481 Processing helix chain 'C' and resid 486 through 506 removed outlier: 3.626A pdb=" N LEU C 499 " --> pdb=" O PHE C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 515 Processing helix chain 'C' and resid 518 through 546 Processing helix chain 'C' and resid 570 through 593 removed outlier: 3.638A pdb=" N ASN C 593 " --> pdb=" O ARG C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 607 Processing helix chain 'C' and resid 609 through 623 Processing helix chain 'C' and resid 661 through 689 removed outlier: 3.582A pdb=" N PHE C 665 " --> pdb=" O ILE C 661 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ALA C 668 " --> pdb=" O MET C 664 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N LEU C 669 " --> pdb=" O PHE C 665 " (cutoff:3.500A) Proline residue: C 670 - end of helix Processing helix chain 'C' and resid 692 through 694 No H-bonds generated for 'chain 'C' and resid 692 through 694' Processing helix chain 'C' and resid 704 through 719 removed outlier: 3.751A pdb=" N LEU C 718 " --> pdb=" O GLY C 714 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE C 719 " --> pdb=" O VAL C 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 728 through 737 Processing helix chain 'C' and resid 761 through 774 removed outlier: 4.826A pdb=" N ILE C 774 " --> pdb=" O VAL C 770 " (cutoff:3.500A) Processing helix chain 'C' and resid 777 through 782 removed outlier: 4.618A pdb=" N ARG C 782 " --> pdb=" O PRO C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 785 through 800 removed outlier: 4.111A pdb=" N LEU C 800 " --> pdb=" O GLY C 796 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 812 Processing helix chain 'C' and resid 823 through 826 No H-bonds generated for 'chain 'C' and resid 823 through 826' Processing helix chain 'C' and resid 830 through 852 Processing helix chain 'C' and resid 856 through 871 removed outlier: 3.501A pdb=" N LEU C 859 " --> pdb=" O SER C 856 " (cutoff:3.500A) Proline residue: C 860 - end of helix Proline residue: C 868 - end of helix Processing helix chain 'C' and resid 873 through 877 removed outlier: 3.746A pdb=" N ILE C 877 " --> pdb=" O LEU C 873 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 873 through 877' Processing helix chain 'C' and resid 880 through 886 Processing helix chain 'E' and resid 380 through 400 Proline residue: E 391 - end of helix removed outlier: 5.214A pdb=" N LEU E 394 " --> pdb=" O TYR E 390 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N SER E 395 " --> pdb=" O PRO E 391 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ALA E 400 " --> pdb=" O ASP E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 431 Proline residue: E 419 - end of helix Processing helix chain 'E' and resid 437 through 454 Processing helix chain 'E' and resid 466 through 482 Processing helix chain 'E' and resid 486 through 506 removed outlier: 3.541A pdb=" N LEU E 499 " --> pdb=" O PHE E 495 " (cutoff:3.500A) Processing helix chain 'E' and resid 509 through 515 removed outlier: 3.560A pdb=" N LEU E 512 " --> pdb=" O GLY E 509 " (cutoff:3.500A) Processing helix chain 'E' and resid 518 through 546 removed outlier: 3.642A pdb=" N LEU E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 592 Processing helix chain 'E' and resid 599 through 607 Processing helix chain 'E' and resid 609 through 623 Processing helix chain 'E' and resid 661 through 689 removed outlier: 3.825A pdb=" N PHE E 665 " --> pdb=" O ILE E 661 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ALA E 668 " --> pdb=" O MET E 664 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LEU E 669 " --> pdb=" O PHE E 665 " (cutoff:3.500A) Proline residue: E 670 - end of helix Processing helix chain 'E' and resid 692 through 694 No H-bonds generated for 'chain 'E' and resid 692 through 694' Processing helix chain 'E' and resid 704 through 718 removed outlier: 3.752A pdb=" N LEU E 718 " --> pdb=" O GLY E 714 " (cutoff:3.500A) Processing helix chain 'E' and resid 728 through 737 Processing helix chain 'E' and resid 761 through 774 removed outlier: 4.762A pdb=" N ILE E 774 " --> pdb=" O VAL E 770 " (cutoff:3.500A) Processing helix chain 'E' and resid 777 through 782 removed outlier: 4.143A pdb=" N ARG E 782 " --> pdb=" O PRO E 778 " (cutoff:3.500A) Processing helix chain 'E' and resid 785 through 800 removed outlier: 4.066A pdb=" N LEU E 800 " --> pdb=" O GLY E 796 " (cutoff:3.500A) Processing helix chain 'E' and resid 804 through 813 removed outlier: 4.041A pdb=" N PHE E 813 " --> pdb=" O ILE E 809 " (cutoff:3.500A) Processing helix chain 'E' and resid 823 through 826 No H-bonds generated for 'chain 'E' and resid 823 through 826' Processing helix chain 'E' and resid 830 through 851 Processing helix chain 'E' and resid 856 through 871 Proline residue: E 860 - end of helix Proline residue: E 868 - end of helix Processing helix chain 'E' and resid 874 through 877 No H-bonds generated for 'chain 'E' and resid 874 through 877' Processing helix chain 'E' and resid 880 through 886 Processing sheet with id= A, first strand: chain 'C' and resid 739 through 741 Processing sheet with id= B, first strand: chain 'E' and resid 739 through 741 496 hydrogen bonds defined for protein. 1428 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: 2.80 Time building geometry restraints manager: 4.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1318 1.32 - 1.44: 2473 1.44 - 1.56: 5510 1.56 - 1.69: 17 1.69 - 1.81: 70 Bond restraints: 9388 Sorted by residual: bond pdb=" C PRO E 815 " pdb=" O PRO E 815 " ideal model delta sigma weight residual 1.246 1.195 0.051 8.50e-03 1.38e+04 3.54e+01 bond pdb=" C PRO C 815 " pdb=" O PRO C 815 " ideal model delta sigma weight residual 1.246 1.196 0.049 8.50e-03 1.38e+04 3.38e+01 bond pdb=" N VAL C 560 " pdb=" CA VAL C 560 " ideal model delta sigma weight residual 1.457 1.497 -0.040 9.00e-03 1.23e+04 1.99e+01 bond pdb=" C1 MAN A 4 " pdb=" C2 MAN A 4 " ideal model delta sigma weight residual 1.526 1.601 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C1B PIO E1004 " pdb=" O3C PIO E1004 " ideal model delta sigma weight residual 1.399 1.326 0.073 2.00e-02 2.50e+03 1.34e+01 ... (remaining 9383 not shown) Histogram of bond angle deviations from ideal: 98.86 - 105.90: 267 105.90 - 112.93: 5204 112.93 - 119.97: 3374 119.97 - 127.00: 3841 127.00 - 134.04: 88 Bond angle restraints: 12774 Sorted by residual: angle pdb=" C ARG D 80 " pdb=" CA ARG D 80 " pdb=" CB ARG D 80 " ideal model delta sigma weight residual 116.54 109.97 6.57 1.15e+00 7.56e-01 3.26e+01 angle pdb=" C TYR C 818 " pdb=" CA TYR C 818 " pdb=" CB TYR C 818 " ideal model delta sigma weight residual 110.79 119.42 -8.63 1.66e+00 3.63e-01 2.70e+01 angle pdb=" N PRO C 598 " pdb=" CA PRO C 598 " pdb=" C PRO C 598 " ideal model delta sigma weight residual 111.14 103.04 8.10 1.56e+00 4.11e-01 2.69e+01 angle pdb=" N GLN E 434 " pdb=" CA GLN E 434 " pdb=" C GLN E 434 " ideal model delta sigma weight residual 111.28 105.84 5.44 1.09e+00 8.42e-01 2.49e+01 angle pdb=" N PRO C 568 " pdb=" CA PRO C 568 " pdb=" C PRO C 568 " ideal model delta sigma weight residual 111.21 118.32 -7.11 1.59e+00 3.96e-01 2.00e+01 ... (remaining 12769 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 4570 17.72 - 35.43: 563 35.43 - 53.15: 180 53.15 - 70.87: 45 70.87 - 88.58: 20 Dihedral angle restraints: 5378 sinusoidal: 2176 harmonic: 3202 Sorted by residual: dihedral pdb=" C TYR C 818 " pdb=" N TYR C 818 " pdb=" CA TYR C 818 " pdb=" CB TYR C 818 " ideal model delta harmonic sigma weight residual -122.60 -132.98 10.38 0 2.50e+00 1.60e-01 1.72e+01 dihedral pdb=" C ASN C 433 " pdb=" N ASN C 433 " pdb=" CA ASN C 433 " pdb=" CB ASN C 433 " ideal model delta harmonic sigma weight residual -122.60 -132.28 9.68 0 2.50e+00 1.60e-01 1.50e+01 dihedral pdb=" C ASN E 433 " pdb=" N ASN E 433 " pdb=" CA ASN E 433 " pdb=" CB ASN E 433 " ideal model delta harmonic sigma weight residual -122.60 -132.17 9.57 0 2.50e+00 1.60e-01 1.47e+01 ... (remaining 5375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1323 0.074 - 0.147: 193 0.147 - 0.221: 34 0.221 - 0.294: 9 0.294 - 0.368: 3 Chirality restraints: 1562 Sorted by residual: chirality pdb=" C1 MAN A 5 " pdb=" O4 BMA A 3 " pdb=" C2 MAN A 5 " pdb=" O5 MAN A 5 " both_signs ideal model delta sigma weight residual False 2.40 2.03 0.37 2.00e-02 2.50e+03 3.39e+02 chirality pdb=" C1 MAN F 5 " pdb=" O4 BMA F 3 " pdb=" C2 MAN F 5 " pdb=" O5 MAN F 5 " both_signs ideal model delta sigma weight residual False 2.40 2.17 0.23 2.00e-02 2.50e+03 1.32e+02 chirality pdb=" CA LYS C 817 " pdb=" N LYS C 817 " pdb=" C LYS C 817 " pdb=" CB LYS C 817 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.82e+00 ... (remaining 1559 not shown) Planarity restraints: 1500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 874 " 0.062 5.00e-02 4.00e+02 9.32e-02 1.39e+01 pdb=" N PRO E 875 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO E 875 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO E 875 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 470 " -0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C VAL C 470 " 0.060 2.00e-02 2.50e+03 pdb=" O VAL C 470 " -0.022 2.00e-02 2.50e+03 pdb=" N PHE C 471 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 429 " 0.017 2.00e-02 2.50e+03 3.34e-02 1.12e+01 pdb=" C GLU E 429 " -0.058 2.00e-02 2.50e+03 pdb=" O GLU E 429 " 0.021 2.00e-02 2.50e+03 pdb=" N LYS E 430 " 0.019 2.00e-02 2.50e+03 ... (remaining 1497 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1939 2.78 - 3.31: 8922 3.31 - 3.84: 16022 3.84 - 4.37: 19092 4.37 - 4.90: 31497 Nonbonded interactions: 77472 Sorted by model distance: nonbonded pdb=" OG1 THR C 375 " pdb=" OE2 GLU C 508 " model vdw 2.251 2.440 nonbonded pdb=" OG SER C 529 " pdb=" OG SER C 799 " model vdw 2.273 2.440 nonbonded pdb=" OD2 ASP C 636 " pdb=" NZ LYS C 639 " model vdw 2.296 2.520 nonbonded pdb=" O SER C 644 " pdb=" NH2 ARG C 656 " model vdw 2.313 2.520 nonbonded pdb=" OG SER C 438 " pdb=" OE2 GLU C 439 " model vdw 2.322 2.440 ... (remaining 77467 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'C' selection = (chain 'E' and (resid 371 through 894 or resid 1001 through 1003)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.190 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: 11.920 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 29.450 Find NCS groups from input model: 0.560 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:12.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 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 : 0.007 0.079 9388 Z= 0.447 Angle : 0.997 10.460 12774 Z= 0.617 Chirality : 0.058 0.368 1562 Planarity : 0.007 0.093 1498 Dihedral : 18.450 88.584 3314 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.27 % Allowed : 1.81 % Favored : 97.91 % Rotamer: Outliers : 3.89 % Allowed : 20.53 % Favored : 75.58 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.45 % 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: 1.10 (0.24), residues: 1102 helix: 1.16 (0.18), residues: 744 sheet: None (None), residues: 0 loop : -0.02 (0.30), residues: 358 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 182 time to evaluate : 1.160 Fit side-chains outliers start: 37 outliers final: 16 residues processed: 206 average time/residue: 1.1853 time to fit residues: 261.4928 Evaluate side-chains 184 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 168 time to evaluate : 1.069 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 13 residues processed: 3 average time/residue: 0.1018 time to fit residues: 1.8659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 550 GLN ** E 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 625 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.0767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9388 Z= 0.189 Angle : 0.569 7.708 12774 Z= 0.273 Chirality : 0.042 0.190 1562 Planarity : 0.006 0.073 1498 Dihedral : 10.313 88.467 1304 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 6.00 % Allowed : 18.53 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.68 (0.24), residues: 1102 helix: 1.67 (0.18), residues: 742 sheet: None (None), residues: 0 loop : 0.05 (0.30), residues: 360 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 176 time to evaluate : 1.040 Fit side-chains revert: symmetry clash outliers start: 57 outliers final: 31 residues processed: 206 average time/residue: 1.1295 time to fit residues: 250.1996 Evaluate side-chains 207 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 176 time to evaluate : 0.967 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 16 residues processed: 15 average time/residue: 0.3231 time to fit residues: 7.2247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 34 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 550 GLN C 564 GLN C 884 GLN E 569 ASN E 625 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9388 Z= 0.341 Angle : 0.630 7.240 12774 Z= 0.303 Chirality : 0.046 0.187 1562 Planarity : 0.006 0.070 1498 Dihedral : 10.087 87.819 1304 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 6.21 % Allowed : 19.05 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.35 (0.24), residues: 1102 helix: 1.32 (0.18), residues: 760 sheet: None (None), residues: 0 loop : 0.10 (0.31), residues: 342 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 166 time to evaluate : 1.068 Fit side-chains revert: symmetry clash outliers start: 59 outliers final: 33 residues processed: 199 average time/residue: 1.1501 time to fit residues: 246.0647 Evaluate side-chains 193 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 160 time to evaluate : 1.052 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 19 residues processed: 14 average time/residue: 0.3130 time to fit residues: 6.8266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 550 GLN C 880 ASN C 884 GLN E 625 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9388 Z= 0.226 Angle : 0.563 7.694 12774 Z= 0.269 Chirality : 0.042 0.173 1562 Planarity : 0.006 0.064 1498 Dihedral : 9.905 88.250 1304 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 6.00 % Allowed : 19.68 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.60 (0.24), residues: 1102 helix: 1.53 (0.18), residues: 746 sheet: None (None), residues: 0 loop : 0.20 (0.31), residues: 356 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 162 time to evaluate : 1.207 Fit side-chains revert: symmetry clash outliers start: 57 outliers final: 32 residues processed: 198 average time/residue: 1.1161 time to fit residues: 238.3678 Evaluate side-chains 194 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 162 time to evaluate : 1.053 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 20 residues processed: 12 average time/residue: 0.2056 time to fit residues: 4.6729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 54 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 550 GLN C 564 GLN E 625 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9388 Z= 0.214 Angle : 0.542 6.596 12774 Z= 0.260 Chirality : 0.042 0.187 1562 Planarity : 0.005 0.062 1498 Dihedral : 9.725 88.565 1304 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 5.89 % Allowed : 19.79 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1102 helix: 1.62 (0.19), residues: 746 sheet: None (None), residues: 0 loop : 0.26 (0.32), residues: 356 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 169 time to evaluate : 1.036 Fit side-chains revert: symmetry clash outliers start: 56 outliers final: 31 residues processed: 201 average time/residue: 1.1959 time to fit residues: 257.6890 Evaluate side-chains 201 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 170 time to evaluate : 1.087 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 20 residues processed: 11 average time/residue: 0.3213 time to fit residues: 5.7466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 26 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 550 GLN C 651 HIS E 434 GLN E 569 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9388 Z= 0.208 Angle : 0.539 8.083 12774 Z= 0.258 Chirality : 0.042 0.186 1562 Planarity : 0.005 0.059 1498 Dihedral : 9.612 88.790 1304 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 5.89 % Allowed : 20.00 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.76 (0.25), residues: 1102 helix: 1.65 (0.19), residues: 746 sheet: None (None), residues: 0 loop : 0.28 (0.32), residues: 356 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 173 time to evaluate : 0.912 Fit side-chains revert: symmetry clash outliers start: 56 outliers final: 34 residues processed: 206 average time/residue: 1.1683 time to fit residues: 258.3212 Evaluate side-chains 206 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 172 time to evaluate : 1.136 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 22 residues processed: 12 average time/residue: 0.3173 time to fit residues: 6.4868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 59 optimal weight: 0.0970 chunk 106 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 550 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9388 Z= 0.160 Angle : 0.513 5.922 12774 Z= 0.245 Chirality : 0.040 0.180 1562 Planarity : 0.005 0.056 1498 Dihedral : 9.343 89.203 1304 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 5.37 % Allowed : 20.42 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.94 (0.25), residues: 1102 helix: 1.80 (0.19), residues: 746 sheet: None (None), residues: 0 loop : 0.31 (0.32), residues: 356 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 183 time to evaluate : 1.096 Fit side-chains revert: symmetry clash outliers start: 51 outliers final: 25 residues processed: 218 average time/residue: 1.1377 time to fit residues: 266.5354 Evaluate side-chains 203 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 178 time to evaluate : 1.059 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 20 residues processed: 5 average time/residue: 0.1237 time to fit residues: 2.3444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 101 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 550 GLN C 884 GLN E 434 GLN E 569 ASN E 625 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9388 Z= 0.205 Angle : 0.538 8.675 12774 Z= 0.258 Chirality : 0.042 0.192 1562 Planarity : 0.005 0.055 1498 Dihedral : 9.270 89.214 1304 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 4.53 % Allowed : 21.68 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1102 helix: 1.73 (0.19), residues: 746 sheet: None (None), residues: 0 loop : 0.30 (0.32), residues: 356 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 175 time to evaluate : 1.563 Fit side-chains revert: symmetry clash outliers start: 43 outliers final: 30 residues processed: 203 average time/residue: 1.2733 time to fit residues: 277.1800 Evaluate side-chains 202 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 172 time to evaluate : 1.077 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 22 residues processed: 8 average time/residue: 0.2457 time to fit residues: 4.0451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.4980 chunk 101 optimal weight: 6.9990 chunk 59 optimal weight: 0.0270 chunk 43 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 30 optimal weight: 9.9990 chunk 89 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 550 GLN C 884 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 9388 Z= 0.147 Angle : 0.499 5.536 12774 Z= 0.242 Chirality : 0.040 0.175 1562 Planarity : 0.005 0.054 1498 Dihedral : 8.949 89.644 1304 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.68 % Allowed : 22.63 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 2.04 (0.25), residues: 1102 helix: 1.90 (0.19), residues: 742 sheet: None (None), residues: 0 loop : 0.32 (0.32), residues: 360 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 179 time to evaluate : 1.033 Fit side-chains revert: symmetry clash outliers start: 35 outliers final: 23 residues processed: 204 average time/residue: 1.1446 time to fit residues: 250.3088 Evaluate side-chains 199 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 176 time to evaluate : 0.981 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 19 residues processed: 5 average time/residue: 0.1136 time to fit residues: 2.2279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 26 optimal weight: 0.0270 overall best weight: 0.9242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 550 GLN C 884 GLN E 434 GLN E 569 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9388 Z= 0.168 Angle : 0.510 9.365 12774 Z= 0.245 Chirality : 0.040 0.173 1562 Planarity : 0.005 0.058 1498 Dihedral : 8.823 89.587 1304 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.32 % Allowed : 24.00 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 2.05 (0.25), residues: 1102 helix: 1.90 (0.19), residues: 742 sheet: None (None), residues: 0 loop : 0.33 (0.32), residues: 360 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 178 time to evaluate : 0.929 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 22 residues processed: 198 average time/residue: 1.0887 time to fit residues: 231.4450 Evaluate side-chains 193 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 171 time to evaluate : 1.000 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 20 residues processed: 3 average time/residue: 0.1132 time to fit residues: 1.9016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 76 optimal weight: 0.3980 chunk 4 optimal weight: 9.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 884 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.139937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.117412 restraints weight = 10151.481| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.37 r_work: 0.3099 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 9388 Z= 0.159 Angle : 0.500 5.537 12774 Z= 0.243 Chirality : 0.040 0.172 1562 Planarity : 0.005 0.062 1498 Dihedral : 8.611 88.150 1304 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.74 % Allowed : 23.89 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 2.07 (0.25), residues: 1102 helix: 1.92 (0.19), residues: 742 sheet: None (None), residues: 0 loop : 0.31 (0.32), residues: 360 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4396.92 seconds wall clock time: 79 minutes 4.41 seconds (4744.41 seconds total)