Starting phenix.real_space_refine on Wed Jun 18 03:39:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8avd_15679/06_2025/8avd_15679.cif Found real_map, /net/cci-nas-00/data/ceres_data/8avd_15679/06_2025/8avd_15679.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8avd_15679/06_2025/8avd_15679.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8avd_15679/06_2025/8avd_15679.map" model { file = "/net/cci-nas-00/data/ceres_data/8avd_15679/06_2025/8avd_15679.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8avd_15679/06_2025/8avd_15679.cif" } resolution = 4.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9439 atoms to isotropic. 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 Ni 3 6.56 5 S 60 5.16 5 C 8127 2.51 5 N 2154 2.21 5 O 2433 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12777 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1077 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain breaks: 1 Chain: "B" Number of atoms: 3181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3181 Classifications: {'peptide': 399} Link IDs: {'PCIS': 3, 'PTRANS': 23, 'TRANS': 372} Chain: "C" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1077 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain breaks: 1 Chain: "D" Number of atoms: 3181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3181 Classifications: {'peptide': 399} Link IDs: {'PCIS': 3, 'PTRANS': 23, 'TRANS': 372} Chain: "E" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1077 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain breaks: 1 Chain: "F" Number of atoms: 3181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3181 Classifications: {'peptide': 399} Link IDs: {'PCIS': 3, 'PTRANS': 23, 'TRANS': 372} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NI': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NI': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.46, per 1000 atoms: 0.58 Number of scatterers: 12777 At special positions: 0 Unit cell: (132.64, 144.246, 126.008, 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) Ni 3 28.00 S 60 16.00 O 2433 8.00 N 2154 7.00 C 8127 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 167 " distance=2.03 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 410 " distance=2.04 Simple disulfide: pdb=" SG CYS B 411 " - pdb=" SG CYS B 416 " distance=2.02 Simple disulfide: pdb=" SG CYS B 434 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS B 526 " distance=2.03 Simple disulfide: pdb=" SG CYS B 486 " - pdb=" SG CYS B 496 " distance=2.06 Simple disulfide: pdb=" SG CYS C 117 " - pdb=" SG CYS C 167 " distance=2.03 Simple disulfide: pdb=" SG CYS D 350 " - pdb=" SG CYS D 410 " distance=2.03 Simple disulfide: pdb=" SG CYS D 411 " - pdb=" SG CYS D 416 " distance=2.03 Simple disulfide: pdb=" SG CYS D 434 " - pdb=" SG CYS D 445 " distance=2.04 Simple disulfide: pdb=" SG CYS D 471 " - pdb=" SG CYS D 526 " distance=2.03 Simple disulfide: pdb=" SG CYS D 486 " - pdb=" SG CYS D 496 " distance=2.02 Simple disulfide: pdb=" SG CYS E 117 " - pdb=" SG CYS E 167 " distance=2.04 Simple disulfide: pdb=" SG CYS F 350 " - pdb=" SG CYS F 410 " distance=2.04 Simple disulfide: pdb=" SG CYS F 411 " - pdb=" SG CYS F 416 " distance=2.03 Simple disulfide: pdb=" SG CYS F 434 " - pdb=" SG CYS F 445 " distance=2.04 Simple disulfide: pdb=" SG CYS F 471 " - pdb=" SG CYS F 526 " distance=2.03 Simple disulfide: pdb=" SG CYS F 486 " - pdb=" SG CYS F 496 " distance=2.08 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.59 Conformation dependent library (CDL) restraints added in 1.9 seconds 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3102 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 30 sheets defined 21.2% alpha, 31.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.17 Creating SS restraints... Processing helix chain 'A' and resid 23 through 44 Processing helix chain 'A' and resid 45 through 50 removed outlier: 4.029A pdb=" N SER A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 88 removed outlier: 3.979A pdb=" N SER A 88 " --> pdb=" O GLN A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 116 Processing helix chain 'A' and resid 130 through 138 removed outlier: 3.691A pdb=" N VAL A 134 " --> pdb=" O SER A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 160 Processing helix chain 'B' and resid 375 through 377 No H-bonds generated for 'chain 'B' and resid 375 through 377' Processing helix chain 'B' and resid 528 through 533 removed outlier: 3.936A pdb=" N VAL B 533 " --> pdb=" O ASP B 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 45 Processing helix chain 'C' and resid 45 through 50 removed outlier: 4.090A pdb=" N SER C 50 " --> pdb=" O SER C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 89 removed outlier: 3.930A pdb=" N SER C 88 " --> pdb=" O GLN C 84 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU C 89 " --> pdb=" O VAL C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 116 Processing helix chain 'C' and resid 130 through 138 removed outlier: 3.518A pdb=" N VAL C 134 " --> pdb=" O SER C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 160 Processing helix chain 'D' and resid 375 through 377 No H-bonds generated for 'chain 'D' and resid 375 through 377' Processing helix chain 'D' and resid 528 through 533 removed outlier: 3.936A pdb=" N VAL D 533 " --> pdb=" O ASP D 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 45 Processing helix chain 'E' and resid 45 through 50 removed outlier: 3.917A pdb=" N SER E 50 " --> pdb=" O SER E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 89 removed outlier: 3.892A pdb=" N SER E 88 " --> pdb=" O GLN E 84 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU E 89 " --> pdb=" O VAL E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 116 Processing helix chain 'E' and resid 130 through 138 Processing helix chain 'E' and resid 138 through 160 Processing helix chain 'F' and resid 375 through 377 No H-bonds generated for 'chain 'F' and resid 375 through 377' Processing helix chain 'F' and resid 528 through 533 removed outlier: 3.920A pdb=" N VAL F 533 " --> pdb=" O ASP F 530 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 58 Processing sheet with id=AA2, first strand: chain 'B' and resid 240 through 246 removed outlier: 6.086A pdb=" N GLY B 241 " --> pdb=" O ASP B 257 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASP B 257 " --> pdb=" O GLY B 241 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 279 through 286 Processing sheet with id=AA4, first strand: chain 'B' and resid 331 through 334 Processing sheet with id=AA5, first strand: chain 'B' and resid 337 through 341 removed outlier: 3.546A pdb=" N ILE B 338 " --> pdb=" O GLU B 422 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 416 through 417 removed outlier: 7.128A pdb=" N CYS B 416 " --> pdb=" O THR C 58 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 432 through 436 Processing sheet with id=AA8, first strand: chain 'B' and resid 482 through 484 removed outlier: 4.264A pdb=" N LEU B 462 " --> pdb=" O LYS B 484 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 482 through 484 removed outlier: 4.264A pdb=" N LEU B 462 " --> pdb=" O LYS B 484 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 539 through 545 removed outlier: 5.344A pdb=" N ASN B 540 " --> pdb=" O GLU B 557 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLU B 557 " --> pdb=" O ASN B 540 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 582 through 586 Processing sheet with id=AB3, first strand: chain 'D' and resid 240 through 246 removed outlier: 5.959A pdb=" N GLY D 241 " --> pdb=" O ASP D 257 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASP D 257 " --> pdb=" O GLY D 241 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 279 through 286 Processing sheet with id=AB5, first strand: chain 'D' and resid 331 through 334 Processing sheet with id=AB6, first strand: chain 'D' and resid 337 through 341 Processing sheet with id=AB7, first strand: chain 'D' and resid 416 through 417 removed outlier: 7.020A pdb=" N CYS D 416 " --> pdb=" O THR E 58 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 433 through 436 Processing sheet with id=AB9, first strand: chain 'D' and resid 482 through 484 removed outlier: 4.759A pdb=" N LEU D 462 " --> pdb=" O LYS D 484 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 482 through 484 removed outlier: 4.759A pdb=" N LEU D 462 " --> pdb=" O LYS D 484 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 539 through 545 removed outlier: 5.262A pdb=" N ASN D 540 " --> pdb=" O GLU D 557 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLU D 557 " --> pdb=" O ASN D 540 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 582 through 586 Processing sheet with id=AC4, first strand: chain 'F' and resid 240 through 246 removed outlier: 6.008A pdb=" N GLY F 241 " --> pdb=" O ASP F 257 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ASP F 257 " --> pdb=" O GLY F 241 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 279 through 286 Processing sheet with id=AC6, first strand: chain 'F' and resid 331 through 334 Processing sheet with id=AC7, first strand: chain 'F' and resid 337 through 341 removed outlier: 3.670A pdb=" N ILE F 338 " --> pdb=" O GLU F 422 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 432 through 436 Processing sheet with id=AC9, first strand: chain 'F' and resid 482 through 483 Processing sheet with id=AD1, first strand: chain 'F' and resid 482 through 483 Processing sheet with id=AD2, first strand: chain 'F' and resid 539 through 545 removed outlier: 5.427A pdb=" N ASN F 540 " --> pdb=" O GLU F 557 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLU F 557 " --> pdb=" O ASN F 540 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 582 through 586 615 hydrogen bonds defined for protein. 1635 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: 4.45 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.30: 2092 1.30 - 1.46: 4085 1.46 - 1.61: 6810 1.61 - 1.76: 1 1.76 - 1.92: 77 Bond restraints: 13065 Sorted by residual: bond pdb=" CG ASN A 103 " pdb=" OD1 ASN A 103 " ideal model delta sigma weight residual 1.231 1.150 0.081 1.90e-02 2.77e+03 1.83e+01 bond pdb=" CG LYS E 74 " pdb=" CD LYS E 74 " ideal model delta sigma weight residual 1.520 1.404 0.116 3.00e-02 1.11e+03 1.50e+01 bond pdb=" CG ASN A 103 " pdb=" ND2 ASN A 103 " ideal model delta sigma weight residual 1.328 1.247 0.081 2.10e-02 2.27e+03 1.48e+01 bond pdb=" CB CYS B 486 " pdb=" SG CYS B 486 " ideal model delta sigma weight residual 1.808 1.917 -0.109 3.30e-02 9.18e+02 1.10e+01 bond pdb=" CB THR C 58 " pdb=" CG2 THR C 58 " ideal model delta sigma weight residual 1.521 1.417 0.104 3.30e-02 9.18e+02 9.85e+00 ... (remaining 13060 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.98: 17738 5.98 - 11.96: 60 11.96 - 17.93: 7 17.93 - 23.91: 2 23.91 - 29.89: 1 Bond angle restraints: 17808 Sorted by residual: angle pdb=" CA CYS F 486 " pdb=" CB CYS F 486 " pdb=" SG CYS F 486 " ideal model delta sigma weight residual 114.40 144.29 -29.89 2.30e+00 1.89e-01 1.69e+02 angle pdb=" CA CYS F 496 " pdb=" CB CYS F 496 " pdb=" SG CYS F 496 " ideal model delta sigma weight residual 114.40 134.97 -20.57 2.30e+00 1.89e-01 8.00e+01 angle pdb=" C CYS F 496 " pdb=" CA CYS F 496 " pdb=" CB CYS F 496 " ideal model delta sigma weight residual 110.16 122.15 -11.99 1.66e+00 3.63e-01 5.22e+01 angle pdb=" CG LYS E 74 " pdb=" CD LYS E 74 " pdb=" CE LYS E 74 " ideal model delta sigma weight residual 111.30 95.52 15.78 2.30e+00 1.89e-01 4.71e+01 angle pdb=" C CYS F 486 " pdb=" CA CYS F 486 " pdb=" CB CYS F 486 " ideal model delta sigma weight residual 109.37 121.89 -12.52 1.83e+00 2.99e-01 4.68e+01 ... (remaining 17803 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 7333 17.65 - 35.30: 511 35.30 - 52.95: 78 52.95 - 70.59: 37 70.59 - 88.24: 12 Dihedral angle restraints: 7971 sinusoidal: 3198 harmonic: 4773 Sorted by residual: dihedral pdb=" CB CYS F 486 " pdb=" SG CYS F 486 " pdb=" SG CYS F 496 " pdb=" CB CYS F 496 " ideal model delta sinusoidal sigma weight residual -86.00 -16.56 -69.44 1 1.00e+01 1.00e-02 6.23e+01 dihedral pdb=" CB CYS B 486 " pdb=" SG CYS B 486 " pdb=" SG CYS B 496 " pdb=" CB CYS B 496 " ideal model delta sinusoidal sigma weight residual 93.00 31.72 61.28 1 1.00e+01 1.00e-02 4.99e+01 dihedral pdb=" C CYS F 486 " pdb=" N CYS F 486 " pdb=" CA CYS F 486 " pdb=" CB CYS F 486 " ideal model delta harmonic sigma weight residual -122.60 -139.14 16.54 0 2.50e+00 1.60e-01 4.38e+01 ... (remaining 7968 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 1979 0.127 - 0.253: 76 0.253 - 0.380: 4 0.380 - 0.507: 1 0.507 - 0.633: 4 Chirality restraints: 2064 Sorted by residual: chirality pdb=" CB THR C 58 " pdb=" CA THR C 58 " pdb=" OG1 THR C 58 " pdb=" CG2 THR C 58 " both_signs ideal model delta sigma weight residual False 2.55 1.92 0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" CB ILE E 69 " pdb=" CA ILE E 69 " pdb=" CG1 ILE E 69 " pdb=" CG2 ILE E 69 " both_signs ideal model delta sigma weight residual False 2.64 2.06 0.59 2.00e-01 2.50e+01 8.59e+00 chirality pdb=" CA CYS F 486 " pdb=" N CYS F 486 " pdb=" C CYS F 486 " pdb=" CB CYS F 486 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.77e+00 ... (remaining 2061 not shown) Planarity restraints: 2259 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 63 " 0.073 5.00e-02 4.00e+02 1.08e-01 1.87e+01 pdb=" N PRO A 64 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO A 64 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO A 64 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 103 " 0.020 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" CG ASN A 103 " -0.073 2.00e-02 2.50e+03 pdb=" OD1 ASN A 103 " 0.028 2.00e-02 2.50e+03 pdb=" ND2 ASN A 103 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE E 63 " 0.059 5.00e-02 4.00e+02 8.74e-02 1.22e+01 pdb=" N PRO E 64 " -0.151 5.00e-02 4.00e+02 pdb=" CA PRO E 64 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO E 64 " 0.047 5.00e-02 4.00e+02 ... (remaining 2256 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 39 2.40 - 3.03: 7364 3.03 - 3.65: 19511 3.65 - 4.28: 28279 4.28 - 4.90: 46720 Nonbonded interactions: 101913 Sorted by model distance: nonbonded pdb=" NH2 ARG E 41 " pdb=" O TYR F 439 " model vdw 1.776 3.120 nonbonded pdb=" ND2 ASN A 103 " pdb=" N LEU B 504 " model vdw 1.888 3.200 nonbonded pdb=" OH TYR B 409 " pdb=" CB SER C 141 " model vdw 1.972 3.440 nonbonded pdb=" NH1 ARG B 512 " pdb=" OD1 ASN B 514 " model vdw 2.071 3.120 nonbonded pdb=" OE1 GLU B 274 " pdb=" NH1 ARG B 280 " model vdw 2.129 3.120 ... (remaining 101908 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 32.240 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 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 : 0.005 0.116 13083 Z= 0.215 Angle : 1.106 29.888 17844 Z= 0.589 Chirality : 0.064 0.633 2064 Planarity : 0.006 0.108 2259 Dihedral : 13.218 88.242 4815 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.25 % Favored : 94.37 % Rotamer: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 9.38 % 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: -0.68 (0.19), residues: 1599 helix: -0.38 (0.26), residues: 300 sheet: 0.20 (0.19), residues: 546 loop : -0.90 (0.21), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 447 HIS 0.007 0.001 HIS C 47 PHE 0.029 0.002 PHE B 502 TYR 0.031 0.003 TYR B 470 ARG 0.029 0.002 ARG B 310 Details of bonding type rmsd hydrogen bonds : bond 0.12041 ( 577) hydrogen bonds : angle 6.73107 ( 1635) SS BOND : bond 0.01468 ( 18) SS BOND : angle 3.71075 ( 36) covalent geometry : bond 0.00489 (13065) covalent geometry : angle 1.09439 (17808) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.9656 (mm) cc_final: 0.9434 (mp) REVERT: A 110 LEU cc_start: 0.8700 (mm) cc_final: 0.8374 (mm) REVERT: A 143 GLU cc_start: 0.9039 (tm-30) cc_final: 0.8797 (tm-30) REVERT: C 30 ASP cc_start: 0.8730 (m-30) cc_final: 0.8506 (m-30) REVERT: C 106 ASP cc_start: 0.8934 (m-30) cc_final: 0.8654 (m-30) REVERT: C 156 ASP cc_start: 0.9073 (m-30) cc_final: 0.8829 (m-30) REVERT: D 584 HIS cc_start: 0.9178 (t70) cc_final: 0.8862 (t-170) REVERT: E 69 ILE cc_start: 0.8398 (tp) cc_final: 0.8122 (pt) REVERT: F 302 TYR cc_start: 0.8494 (m-80) cc_final: 0.8049 (m-80) REVERT: F 366 TRP cc_start: 0.7657 (m100) cc_final: 0.7429 (m100) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.2133 time to fit residues: 47.5417 Evaluate side-chains 92 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 6.9990 chunk 120 optimal weight: 0.0980 chunk 66 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 64 optimal weight: 7.9990 chunk 124 optimal weight: 0.6980 chunk 48 optimal weight: 8.9990 chunk 75 optimal weight: 50.0000 chunk 92 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A 103 ASN A 159 GLN B 324 GLN B 461 GLN ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 ASN E 67 HIS E 103 ASN E 155 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.076414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.060611 restraints weight = 71804.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.061041 restraints weight = 39690.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.062359 restraints weight = 26247.517| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 13083 Z= 0.151 Angle : 0.675 13.290 17844 Z= 0.348 Chirality : 0.047 0.365 2064 Planarity : 0.004 0.049 2259 Dihedral : 5.477 65.051 1740 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.20 % Allowed : 2.69 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 0.62 (0.20), residues: 1599 helix: 1.35 (0.29), residues: 306 sheet: 0.70 (0.19), residues: 540 loop : -0.12 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 556 HIS 0.011 0.001 HIS E 67 PHE 0.008 0.001 PHE B 502 TYR 0.016 0.001 TYR B 470 ARG 0.006 0.001 ARG F 280 Details of bonding type rmsd hydrogen bonds : bond 0.04227 ( 577) hydrogen bonds : angle 5.64921 ( 1635) SS BOND : bond 0.00497 ( 18) SS BOND : angle 1.86637 ( 36) covalent geometry : bond 0.00330 (13065) covalent geometry : angle 0.67066 (17808) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 130 time to evaluate : 1.631 Fit side-chains revert: symmetry clash REVERT: A 102 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8604 (mm-30) REVERT: A 143 GLU cc_start: 0.9255 (tm-30) cc_final: 0.8929 (tm-30) REVERT: C 37 THR cc_start: 0.9552 (m) cc_final: 0.9246 (m) REVERT: C 106 ASP cc_start: 0.8946 (m-30) cc_final: 0.8686 (m-30) REVERT: C 156 ASP cc_start: 0.9168 (m-30) cc_final: 0.8947 (m-30) REVERT: D 252 LEU cc_start: 0.9005 (tt) cc_final: 0.8753 (tt) REVERT: D 584 HIS cc_start: 0.9088 (t70) cc_final: 0.8748 (t-170) REVERT: E 35 ILE cc_start: 0.9698 (mt) cc_final: 0.9284 (tt) REVERT: F 302 TYR cc_start: 0.8433 (m-80) cc_final: 0.8076 (m-80) REVERT: F 366 TRP cc_start: 0.7680 (m100) cc_final: 0.7190 (m100) outliers start: 3 outliers final: 1 residues processed: 133 average time/residue: 0.3369 time to fit residues: 70.3627 Evaluate side-chains 83 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 82 time to evaluate : 2.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 9 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 132 optimal weight: 0.1980 chunk 45 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 119 optimal weight: 0.5980 chunk 123 optimal weight: 7.9990 chunk 145 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 461 GLN ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.075562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.059471 restraints weight = 70982.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.060217 restraints weight = 38994.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.061311 restraints weight = 25373.170| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13083 Z= 0.122 Angle : 0.607 12.860 17844 Z= 0.311 Chirality : 0.044 0.243 2064 Planarity : 0.004 0.030 2259 Dihedral : 5.143 63.598 1740 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.13 % Allowed : 2.28 % Favored : 97.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 1.06 (0.21), residues: 1599 helix: 1.78 (0.29), residues: 306 sheet: 0.80 (0.19), residues: 593 loop : 0.25 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 366 HIS 0.005 0.001 HIS A 67 PHE 0.007 0.001 PHE F 334 TYR 0.013 0.001 TYR D 424 ARG 0.008 0.000 ARG F 280 Details of bonding type rmsd hydrogen bonds : bond 0.03852 ( 577) hydrogen bonds : angle 5.30080 ( 1635) SS BOND : bond 0.00297 ( 18) SS BOND : angle 1.95424 ( 36) covalent geometry : bond 0.00268 (13065) covalent geometry : angle 0.60169 (17808) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 126 time to evaluate : 2.023 Fit side-chains REVERT: A 102 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8513 (mm-30) REVERT: A 110 LEU cc_start: 0.8844 (mm) cc_final: 0.8466 (mm) REVERT: A 143 GLU cc_start: 0.9255 (tm-30) cc_final: 0.8990 (tm-30) REVERT: B 461 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.8777 (pp30) REVERT: C 36 LYS cc_start: 0.9038 (pptt) cc_final: 0.8834 (pptt) REVERT: C 37 THR cc_start: 0.9525 (m) cc_final: 0.9169 (m) REVERT: C 106 ASP cc_start: 0.8938 (m-30) cc_final: 0.8665 (m-30) REVERT: C 156 ASP cc_start: 0.9139 (m-30) cc_final: 0.8833 (m-30) REVERT: D 252 LEU cc_start: 0.8966 (tt) cc_final: 0.8717 (tt) REVERT: D 584 HIS cc_start: 0.9124 (t70) cc_final: 0.8785 (t-170) REVERT: E 35 ILE cc_start: 0.9704 (mt) cc_final: 0.9307 (tt) REVERT: E 76 ASP cc_start: 0.8809 (t0) cc_final: 0.8575 (t0) REVERT: E 95 LEU cc_start: 0.9566 (mt) cc_final: 0.9344 (mt) REVERT: F 302 TYR cc_start: 0.8496 (m-80) cc_final: 0.8113 (m-80) REVERT: F 366 TRP cc_start: 0.7632 (m100) cc_final: 0.7199 (m100) outliers start: 2 outliers final: 0 residues processed: 128 average time/residue: 0.2885 time to fit residues: 58.4087 Evaluate side-chains 88 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 87 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 7 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 121 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 138 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 461 GLN E 43 ASN ** E 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.072222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.056657 restraints weight = 72074.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.056287 restraints weight = 39595.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.057474 restraints weight = 29901.264| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13083 Z= 0.183 Angle : 0.651 10.275 17844 Z= 0.334 Chirality : 0.044 0.235 2064 Planarity : 0.004 0.041 2259 Dihedral : 5.346 69.358 1740 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.13 % Allowed : 4.30 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 1.05 (0.21), residues: 1599 helix: 1.64 (0.29), residues: 306 sheet: 0.79 (0.20), residues: 594 loop : 0.32 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 367 HIS 0.007 0.001 HIS E 109 PHE 0.012 0.001 PHE D 403 TYR 0.014 0.002 TYR B 470 ARG 0.011 0.001 ARG D 310 Details of bonding type rmsd hydrogen bonds : bond 0.03907 ( 577) hydrogen bonds : angle 5.38054 ( 1635) SS BOND : bond 0.00523 ( 18) SS BOND : angle 2.03126 ( 36) covalent geometry : bond 0.00388 (13065) covalent geometry : angle 0.64562 (17808) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 115 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.8954 (m-30) cc_final: 0.8739 (m-30) REVERT: A 102 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8470 (mm-30) REVERT: A 143 GLU cc_start: 0.9334 (tm-30) cc_final: 0.9008 (tm-30) REVERT: C 37 THR cc_start: 0.9512 (m) cc_final: 0.9140 (m) REVERT: C 156 ASP cc_start: 0.9073 (m-30) cc_final: 0.8750 (m-30) REVERT: D 584 HIS cc_start: 0.9263 (t70) cc_final: 0.8862 (t-170) REVERT: E 35 ILE cc_start: 0.9636 (mt) cc_final: 0.9367 (tt) REVERT: E 76 ASP cc_start: 0.8767 (t0) cc_final: 0.8548 (t0) REVERT: F 366 TRP cc_start: 0.7934 (m100) cc_final: 0.7474 (m100) outliers start: 2 outliers final: 1 residues processed: 116 average time/residue: 0.2574 time to fit residues: 48.2550 Evaluate side-chains 87 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 1.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 21 optimal weight: 20.0000 chunk 89 optimal weight: 0.5980 chunk 125 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 76 optimal weight: 20.0000 chunk 62 optimal weight: 0.9990 chunk 136 optimal weight: 0.8980 chunk 3 optimal weight: 0.0980 chunk 45 optimal weight: 8.9990 chunk 48 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 461 GLN ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 478 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.072550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.055874 restraints weight = 68965.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.057657 restraints weight = 46754.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.058822 restraints weight = 23436.565| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13083 Z= 0.108 Angle : 0.603 13.790 17844 Z= 0.306 Chirality : 0.044 0.213 2064 Planarity : 0.004 0.073 2259 Dihedral : 5.058 60.353 1740 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.07 % Allowed : 1.48 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.19 (0.21), residues: 1599 helix: 1.81 (0.30), residues: 306 sheet: 0.80 (0.19), residues: 606 loop : 0.44 (0.26), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 367 HIS 0.007 0.001 HIS C 109 PHE 0.012 0.001 PHE F 334 TYR 0.010 0.001 TYR F 424 ARG 0.013 0.001 ARG F 280 Details of bonding type rmsd hydrogen bonds : bond 0.03614 ( 577) hydrogen bonds : angle 5.07524 ( 1635) SS BOND : bond 0.00267 ( 18) SS BOND : angle 2.11751 ( 36) covalent geometry : bond 0.00233 (13065) covalent geometry : angle 0.59586 (17808) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 1.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.8926 (m-30) cc_final: 0.8689 (m-30) REVERT: A 102 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8362 (mm-30) REVERT: A 110 LEU cc_start: 0.8622 (mm) cc_final: 0.8280 (mm) REVERT: A 143 GLU cc_start: 0.9340 (tm-30) cc_final: 0.8979 (tm-30) REVERT: B 461 GLN cc_start: 0.9035 (OUTLIER) cc_final: 0.8670 (pp30) REVERT: B 632 MET cc_start: 0.4646 (ptt) cc_final: 0.4183 (ptt) REVERT: C 30 ASP cc_start: 0.8950 (m-30) cc_final: 0.8748 (m-30) REVERT: C 36 LYS cc_start: 0.9073 (pptt) cc_final: 0.8866 (pptt) REVERT: C 37 THR cc_start: 0.9569 (m) cc_final: 0.9222 (m) REVERT: C 106 ASP cc_start: 0.8835 (t0) cc_final: 0.8447 (t0) REVERT: C 156 ASP cc_start: 0.9024 (m-30) cc_final: 0.8694 (m-30) REVERT: D 584 HIS cc_start: 0.9189 (t70) cc_final: 0.8951 (t70) REVERT: E 76 ASP cc_start: 0.8906 (t0) cc_final: 0.8657 (t0) REVERT: F 302 TYR cc_start: 0.8551 (m-80) cc_final: 0.8188 (m-80) REVERT: F 366 TRP cc_start: 0.7664 (m100) cc_final: 0.7406 (m100) outliers start: 1 outliers final: 0 residues processed: 116 average time/residue: 0.2196 time to fit residues: 39.3955 Evaluate side-chains 87 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 114 optimal weight: 0.7980 chunk 139 optimal weight: 0.4980 chunk 104 optimal weight: 5.9990 chunk 117 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 chunk 79 optimal weight: 0.0870 chunk 141 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 461 GLN ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN ** E 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 ASN F 465 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.073142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.057113 restraints weight = 67136.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.059208 restraints weight = 47943.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.059168 restraints weight = 25187.889| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13083 Z= 0.106 Angle : 0.591 11.227 17844 Z= 0.299 Chirality : 0.044 0.213 2064 Planarity : 0.004 0.059 2259 Dihedral : 4.940 64.108 1740 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.13 % Allowed : 1.88 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.21 (0.21), residues: 1599 helix: 1.82 (0.30), residues: 306 sheet: 0.83 (0.20), residues: 604 loop : 0.45 (0.25), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 556 HIS 0.003 0.001 HIS F 349 PHE 0.022 0.001 PHE D 326 TYR 0.011 0.001 TYR B 333 ARG 0.008 0.000 ARG E 105 Details of bonding type rmsd hydrogen bonds : bond 0.03487 ( 577) hydrogen bonds : angle 4.90755 ( 1635) SS BOND : bond 0.00220 ( 18) SS BOND : angle 2.03079 ( 36) covalent geometry : bond 0.00229 (13065) covalent geometry : angle 0.58410 (17808) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 116 time to evaluate : 1.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8351 (mm-30) REVERT: A 110 LEU cc_start: 0.8647 (mm) cc_final: 0.8262 (mm) REVERT: B 461 GLN cc_start: 0.9068 (OUTLIER) cc_final: 0.8742 (pp30) REVERT: C 30 ASP cc_start: 0.8935 (m-30) cc_final: 0.8732 (m-30) REVERT: C 36 LYS cc_start: 0.9134 (pptt) cc_final: 0.8896 (pptt) REVERT: C 37 THR cc_start: 0.9570 (m) cc_final: 0.9259 (m) REVERT: C 106 ASP cc_start: 0.8857 (t0) cc_final: 0.8453 (t0) REVERT: C 156 ASP cc_start: 0.8926 (m-30) cc_final: 0.8578 (m-30) REVERT: D 584 HIS cc_start: 0.9200 (t70) cc_final: 0.8964 (t70) REVERT: E 95 LEU cc_start: 0.9540 (mt) cc_final: 0.9339 (mt) REVERT: F 302 TYR cc_start: 0.8589 (m-80) cc_final: 0.8276 (m-80) REVERT: F 366 TRP cc_start: 0.7720 (m100) cc_final: 0.7417 (m100) outliers start: 2 outliers final: 0 residues processed: 117 average time/residue: 0.2029 time to fit residues: 37.9564 Evaluate side-chains 89 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 22 optimal weight: 50.0000 chunk 147 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 102 optimal weight: 10.0000 chunk 129 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 GLN ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 GLN D 305 GLN ** E 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 ASN F 305 GLN F 461 GLN F 567 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.068660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.053212 restraints weight = 74865.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.053933 restraints weight = 50619.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.054731 restraints weight = 26317.113| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13083 Z= 0.250 Angle : 0.734 13.053 17844 Z= 0.379 Chirality : 0.046 0.388 2064 Planarity : 0.005 0.075 2259 Dihedral : 5.524 76.002 1740 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.13 % Allowed : 1.41 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 0.90 (0.21), residues: 1599 helix: 1.30 (0.28), residues: 303 sheet: 0.74 (0.21), residues: 576 loop : 0.32 (0.25), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 366 HIS 0.015 0.002 HIS F 478 PHE 0.014 0.002 PHE D 403 TYR 0.020 0.002 TYR F 619 ARG 0.007 0.001 ARG A 41 Details of bonding type rmsd hydrogen bonds : bond 0.04224 ( 577) hydrogen bonds : angle 5.61659 ( 1635) SS BOND : bond 0.00347 ( 18) SS BOND : angle 1.97202 ( 36) covalent geometry : bond 0.00519 (13065) covalent geometry : angle 0.72895 (17808) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 104 time to evaluate : 1.498 Fit side-chains revert: symmetry clash REVERT: C 30 ASP cc_start: 0.8952 (m-30) cc_final: 0.8744 (m-30) REVERT: C 106 ASP cc_start: 0.9231 (t0) cc_final: 0.8937 (t0) REVERT: C 156 ASP cc_start: 0.9026 (m-30) cc_final: 0.8723 (m-30) REVERT: D 320 TRP cc_start: 0.7655 (m100) cc_final: 0.7398 (m100) REVERT: D 584 HIS cc_start: 0.9257 (t70) cc_final: 0.9056 (t70) REVERT: D 600 ASP cc_start: 0.8658 (p0) cc_final: 0.8418 (t70) REVERT: E 61 ASP cc_start: 0.8471 (p0) cc_final: 0.8243 (p0) REVERT: F 366 TRP cc_start: 0.8435 (m100) cc_final: 0.8215 (m100) REVERT: F 632 MET cc_start: 0.2059 (tmm) cc_final: 0.1516 (ttt) outliers start: 2 outliers final: 1 residues processed: 105 average time/residue: 0.2194 time to fit residues: 35.7486 Evaluate side-chains 72 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 95 optimal weight: 0.5980 chunk 89 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 157 optimal weight: 10.0000 chunk 120 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 14 optimal weight: 20.0000 chunk 92 optimal weight: 9.9990 chunk 107 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 GLN E 43 ASN ** E 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.070228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.053142 restraints weight = 73587.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.055088 restraints weight = 48077.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.055715 restraints weight = 23836.824| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13083 Z= 0.119 Angle : 0.626 12.244 17844 Z= 0.320 Chirality : 0.045 0.226 2064 Planarity : 0.005 0.127 2259 Dihedral : 5.169 67.466 1740 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.07 % Allowed : 0.87 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 1.11 (0.22), residues: 1599 helix: 1.70 (0.30), residues: 303 sheet: 0.72 (0.20), residues: 601 loop : 0.47 (0.26), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 366 HIS 0.004 0.001 HIS B 349 PHE 0.020 0.001 PHE D 493 TYR 0.036 0.001 TYR C 82 ARG 0.011 0.001 ARG D 446 Details of bonding type rmsd hydrogen bonds : bond 0.03720 ( 577) hydrogen bonds : angle 5.11623 ( 1635) SS BOND : bond 0.00232 ( 18) SS BOND : angle 1.78010 ( 36) covalent geometry : bond 0.00261 (13065) covalent geometry : angle 0.62155 (17808) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 106 time to evaluate : 1.539 Fit side-chains revert: symmetry clash REVERT: C 30 ASP cc_start: 0.8968 (m-30) cc_final: 0.8763 (m-30) REVERT: C 36 LYS cc_start: 0.9021 (pptt) cc_final: 0.8728 (pptt) REVERT: C 37 THR cc_start: 0.9575 (m) cc_final: 0.9284 (m) REVERT: C 106 ASP cc_start: 0.8913 (t0) cc_final: 0.8556 (t0) REVERT: C 156 ASP cc_start: 0.8985 (m-30) cc_final: 0.8687 (m-30) REVERT: D 320 TRP cc_start: 0.7703 (m100) cc_final: 0.7392 (m100) REVERT: F 366 TRP cc_start: 0.7942 (m100) cc_final: 0.7698 (m100) outliers start: 1 outliers final: 0 residues processed: 107 average time/residue: 0.2250 time to fit residues: 38.6078 Evaluate side-chains 75 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 148 optimal weight: 0.2980 chunk 6 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 chunk 147 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 102 optimal weight: 0.0570 chunk 76 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 overall best weight: 0.6302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 GLN E 43 ASN ** E 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.070500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.053375 restraints weight = 72685.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.055110 restraints weight = 46706.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.055598 restraints weight = 24909.927| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13083 Z= 0.109 Angle : 0.609 11.690 17844 Z= 0.309 Chirality : 0.044 0.219 2064 Planarity : 0.004 0.105 2259 Dihedral : 5.021 64.255 1740 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.07 % Allowed : 0.54 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.19 (0.22), residues: 1599 helix: 1.78 (0.30), residues: 303 sheet: 0.77 (0.20), residues: 601 loop : 0.52 (0.26), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 447 HIS 0.003 0.001 HIS B 349 PHE 0.013 0.001 PHE F 334 TYR 0.029 0.001 TYR C 82 ARG 0.007 0.001 ARG D 446 Details of bonding type rmsd hydrogen bonds : bond 0.03531 ( 577) hydrogen bonds : angle 4.94731 ( 1635) SS BOND : bond 0.00262 ( 18) SS BOND : angle 2.07499 ( 36) covalent geometry : bond 0.00241 (13065) covalent geometry : angle 0.60226 (17808) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 1.392 Fit side-chains REVERT: A 101 LEU cc_start: 0.9535 (mt) cc_final: 0.9326 (mt) REVERT: A 102 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8327 (mm-30) REVERT: C 30 ASP cc_start: 0.8998 (m-30) cc_final: 0.8778 (m-30) REVERT: C 36 LYS cc_start: 0.9024 (pptt) cc_final: 0.8741 (pptt) REVERT: C 37 THR cc_start: 0.9596 (m) cc_final: 0.9326 (m) REVERT: C 106 ASP cc_start: 0.8907 (t0) cc_final: 0.8540 (t0) REVERT: C 156 ASP cc_start: 0.9003 (m-30) cc_final: 0.8721 (m-30) REVERT: D 320 TRP cc_start: 0.7694 (m100) cc_final: 0.7365 (m100) REVERT: D 584 HIS cc_start: 0.9464 (t70) cc_final: 0.9215 (t70) REVERT: E 61 ASP cc_start: 0.8184 (p0) cc_final: 0.7751 (m-30) REVERT: F 366 TRP cc_start: 0.7956 (m100) cc_final: 0.7697 (m100) outliers start: 1 outliers final: 0 residues processed: 109 average time/residue: 0.1941 time to fit residues: 34.1099 Evaluate side-chains 76 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.2097 > 50: distance: 40 - 45: 5.245 distance: 45 - 46: 23.012 distance: 46 - 47: 25.293 distance: 46 - 49: 4.439 distance: 47 - 48: 15.163 distance: 47 - 54: 19.149 distance: 49 - 50: 8.092 distance: 50 - 51: 33.578 distance: 51 - 52: 10.817 distance: 51 - 53: 45.001 distance: 54 - 55: 6.286 distance: 55 - 56: 19.089 distance: 55 - 58: 32.928 distance: 56 - 57: 7.000 distance: 56 - 62: 4.630 distance: 58 - 59: 15.717 distance: 59 - 60: 15.689 distance: 59 - 61: 13.451 distance: 62 - 63: 5.401 distance: 63 - 64: 7.052 distance: 63 - 66: 15.792 distance: 64 - 65: 8.459 distance: 64 - 70: 17.109 distance: 66 - 67: 24.898 distance: 67 - 68: 8.815 distance: 67 - 69: 7.810 distance: 70 - 71: 18.382 distance: 71 - 72: 7.496 distance: 71 - 74: 21.536 distance: 72 - 73: 5.681 distance: 72 - 78: 8.041 distance: 74 - 75: 12.325 distance: 75 - 76: 14.485 distance: 75 - 77: 45.456 distance: 78 - 79: 11.125 distance: 78 - 268: 8.416 distance: 79 - 80: 9.229 distance: 79 - 82: 8.257 distance: 80 - 81: 7.303 distance: 80 - 87: 4.171 distance: 81 - 265: 5.564 distance: 82 - 83: 4.732 distance: 83 - 84: 7.639 distance: 84 - 85: 10.065 distance: 87 - 88: 4.802 distance: 87 - 192: 3.450 distance: 88 - 89: 6.213 distance: 88 - 91: 8.171 distance: 90 - 189: 12.450 distance: 91 - 92: 7.830 distance: 92 - 93: 11.776 distance: 92 - 94: 20.139 distance: 93 - 95: 7.444 distance: 94 - 96: 3.702 distance: 95 - 97: 19.696 distance: 96 - 97: 11.310 distance: 98 - 99: 4.148 distance: 98 - 251: 11.777 distance: 99 - 100: 4.521 distance: 100 - 101: 5.571 distance: 100 - 107: 8.450 distance: 101 - 248: 10.806 distance: 103 - 104: 3.785 distance: 104 - 105: 4.632 distance: 104 - 106: 7.854 distance: 107 - 108: 5.160 distance: 107 - 177: 5.902 distance: 108 - 111: 5.453 distance: 109 - 110: 9.093 distance: 109 - 115: 7.918 distance: 110 - 174: 14.271 distance: 111 - 112: 6.462 distance: 112 - 114: 3.126 distance: 115 - 116: 3.364 distance: 115 - 235: 9.480 distance: 116 - 119: 4.969 distance: 117 - 118: 3.181 distance: 117 - 126: 4.168 distance: 118 - 232: 7.617 distance: 119 - 120: 6.696 distance: 120 - 121: 6.684 distance: 121 - 122: 4.668 distance: 122 - 123: 3.316 distance: 123 - 124: 3.701 distance: 123 - 125: 3.357 distance: 126 - 127: 7.055 distance: 126 - 162: 7.678 distance: 127 - 128: 6.433 distance: 127 - 130: 4.083 distance: 128 - 129: 5.561 distance: 129 - 159: 5.130 distance: 131 - 133: 8.384 distance: 134 - 136: 6.192 distance: 135 - 136: 7.064 distance: 136 - 137: 4.401