Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 14:53:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tti_26116/04_2023/7tti_26116_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tti_26116/04_2023/7tti_26116.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tti_26116/04_2023/7tti_26116_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tti_26116/04_2023/7tti_26116_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tti_26116/04_2023/7tti_26116_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tti_26116/04_2023/7tti_26116.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tti_26116/04_2023/7tti_26116.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tti_26116/04_2023/7tti_26116_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tti_26116/04_2023/7tti_26116_trim_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 5030 2.51 5 N 1208 2.21 5 O 1370 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 222": "OE1" <-> "OE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 7670 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 3753 Classifications: {'peptide': 542} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 27, 'TRANS': 514} Unresolved non-hydrogen bonds: 370 Unresolved non-hydrogen angles: 464 Unresolved non-hydrogen dihedrals: 316 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 11, 'TYR:plan': 5, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 7, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 233 Chain: "B" Number of atoms: 3753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 3753 Classifications: {'peptide': 542} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 27, 'TRANS': 514} Unresolved non-hydrogen bonds: 370 Unresolved non-hydrogen angles: 464 Unresolved non-hydrogen dihedrals: 316 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 11, 'TYR:plan': 5, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 7, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 233 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'JUX': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'JUX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.60, per 1000 atoms: 0.60 Number of scatterers: 7670 At special positions: 0 Unit cell: (85.905, 108.675, 104.535, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 1370 8.00 N 1208 7.00 C 5030 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 626 " distance=2.03 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 353 " distance=2.03 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 626 " distance=2.03 Simple disulfide: pdb=" SG CYS B 308 " - pdb=" SG CYS B 323 " distance=2.03 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 353 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN A 312 " " NAG D 1 " - " ASN A 361 " " NAG E 1 " - " ASN B 312 " " NAG F 1 " - " ASN B 361 " Time building additional restraints: 3.55 Conformation dependent library (CDL) restraints added in 1.3 seconds 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1984 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 2 sheets defined 62.9% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 121 through 133 removed outlier: 4.442A pdb=" N LEU A 126 " --> pdb=" O MET A 122 " (cutoff:3.500A) Proline residue: A 127 - end of helix removed outlier: 3.522A pdb=" N PHE A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 177 removed outlier: 6.586A pdb=" N VAL A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N LEU A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASN A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 192 Processing helix chain 'A' and resid 195 through 226 removed outlier: 3.841A pdb=" N ALA A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 Proline residue: A 237 - end of helix Processing helix chain 'A' and resid 244 through 267 removed outlier: 3.849A pdb=" N THR A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE A 261 " --> pdb=" O ILE A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 274 through 300 Processing helix chain 'A' and resid 337 through 340 No H-bonds generated for 'chain 'A' and resid 337 through 340' Processing helix chain 'A' and resid 355 through 359 Processing helix chain 'A' and resid 373 through 378 Processing helix chain 'A' and resid 420 through 431 Proline residue: A 429 - end of helix Processing helix chain 'A' and resid 436 through 439 No H-bonds generated for 'chain 'A' and resid 436 through 439' Processing helix chain 'A' and resid 447 through 449 No H-bonds generated for 'chain 'A' and resid 447 through 449' Processing helix chain 'A' and resid 451 through 476 Processing helix chain 'A' and resid 479 through 482 No H-bonds generated for 'chain 'A' and resid 479 through 482' Processing helix chain 'A' and resid 485 through 487 No H-bonds generated for 'chain 'A' and resid 485 through 487' Processing helix chain 'A' and resid 495 through 499 removed outlier: 3.569A pdb=" N LEU A 499 " --> pdb=" O VAL A 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 495 through 499' Processing helix chain 'A' and resid 504 through 535 Proline residue: A 527 - end of helix Processing helix chain 'A' and resid 540 through 542 No H-bonds generated for 'chain 'A' and resid 540 through 542' Processing helix chain 'A' and resid 550 through 552 No H-bonds generated for 'chain 'A' and resid 550 through 552' Processing helix chain 'A' and resid 558 through 571 Processing helix chain 'A' and resid 579 through 601 Processing helix chain 'A' and resid 614 through 655 removed outlier: 4.254A pdb=" N MET A 630 " --> pdb=" O CYS A 626 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N TYR A 636 " --> pdb=" O VAL A 632 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N TYR A 637 " --> pdb=" O SER A 633 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL A 640 " --> pdb=" O TYR A 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 133 removed outlier: 4.428A pdb=" N LEU B 126 " --> pdb=" O MET B 122 " (cutoff:3.500A) Proline residue: B 127 - end of helix Processing helix chain 'B' and resid 140 through 177 removed outlier: 6.569A pdb=" N VAL B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N LEU B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN B 152 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASN B 177 " --> pdb=" O ALA B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 195 through 226 removed outlier: 3.763A pdb=" N ALA B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 239 Proline residue: B 237 - end of helix Processing helix chain 'B' and resid 244 through 267 removed outlier: 3.866A pdb=" N THR B 256 " --> pdb=" O ARG B 252 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE B 261 " --> pdb=" O ILE B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' Processing helix chain 'B' and resid 274 through 300 Processing helix chain 'B' and resid 337 through 340 No H-bonds generated for 'chain 'B' and resid 337 through 340' Processing helix chain 'B' and resid 355 through 359 Processing helix chain 'B' and resid 373 through 378 Processing helix chain 'B' and resid 420 through 431 Proline residue: B 429 - end of helix Processing helix chain 'B' and resid 436 through 439 No H-bonds generated for 'chain 'B' and resid 436 through 439' Processing helix chain 'B' and resid 447 through 449 No H-bonds generated for 'chain 'B' and resid 447 through 449' Processing helix chain 'B' and resid 451 through 476 Processing helix chain 'B' and resid 479 through 482 No H-bonds generated for 'chain 'B' and resid 479 through 482' Processing helix chain 'B' and resid 485 through 487 No H-bonds generated for 'chain 'B' and resid 485 through 487' Processing helix chain 'B' and resid 495 through 499 removed outlier: 3.564A pdb=" N LEU B 499 " --> pdb=" O VAL B 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 495 through 499' Processing helix chain 'B' and resid 504 through 535 Proline residue: B 527 - end of helix Processing helix chain 'B' and resid 540 through 542 No H-bonds generated for 'chain 'B' and resid 540 through 542' Processing helix chain 'B' and resid 550 through 552 No H-bonds generated for 'chain 'B' and resid 550 through 552' Processing helix chain 'B' and resid 558 through 571 Processing helix chain 'B' and resid 579 through 601 Processing helix chain 'B' and resid 614 through 655 removed outlier: 4.249A pdb=" N MET B 630 " --> pdb=" O CYS B 626 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N TYR B 636 " --> pdb=" O VAL B 632 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N TYR B 637 " --> pdb=" O SER B 633 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL B 640 " --> pdb=" O TYR B 636 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 306 through 310 Processing sheet with id= B, first strand: chain 'B' and resid 306 through 310 459 hydrogen bonds defined for protein. 1371 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.04 Time building geometry restraints manager: 3.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2346 1.34 - 1.46: 1915 1.46 - 1.58: 3503 1.58 - 1.70: 0 1.70 - 1.82: 88 Bond restraints: 7852 Sorted by residual: bond pdb=" C6 JUX A1201 " pdb=" N2 JUX A1201 " ideal model delta sigma weight residual 1.567 1.340 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C6 JUX B1201 " pdb=" N2 JUX B1201 " ideal model delta sigma weight residual 1.567 1.340 0.227 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C5 JUX B1201 " pdb=" S1 JUX B1201 " ideal model delta sigma weight residual 1.546 1.400 0.146 2.00e-02 2.50e+03 5.36e+01 bond pdb=" C5 JUX A1201 " pdb=" S1 JUX A1201 " ideal model delta sigma weight residual 1.546 1.400 0.146 2.00e-02 2.50e+03 5.33e+01 bond pdb=" C8 JUX A1201 " pdb=" S1 JUX A1201 " ideal model delta sigma weight residual 1.519 1.394 0.125 2.00e-02 2.50e+03 3.88e+01 ... (remaining 7847 not shown) Histogram of bond angle deviations from ideal: 58.91 - 74.11: 6 74.11 - 89.31: 0 89.31 - 104.52: 158 104.52 - 119.72: 6650 119.72 - 134.92: 3990 Bond angle restraints: 10804 Sorted by residual: angle pdb=" CE1 JUX B1201 " pdb=" S2 JUX B1201 " pdb=" C9 JUX B1201 " ideal model delta sigma weight residual 109.49 95.65 13.84 3.00e+00 1.11e-01 2.13e+01 angle pdb=" CE1 JUX A1201 " pdb=" S2 JUX A1201 " pdb=" C9 JUX A1201 " ideal model delta sigma weight residual 109.49 95.84 13.65 3.00e+00 1.11e-01 2.07e+01 angle pdb=" C5 JUX B1201 " pdb=" S1 JUX B1201 " pdb=" C8 JUX B1201 " ideal model delta sigma weight residual 107.48 95.71 11.77 3.00e+00 1.11e-01 1.54e+01 angle pdb=" C5 JUX A1201 " pdb=" S1 JUX A1201 " pdb=" C8 JUX A1201 " ideal model delta sigma weight residual 107.48 95.75 11.73 3.00e+00 1.11e-01 1.53e+01 angle pdb=" N2 JUX B1201 " pdb=" C5 JUX B1201 " pdb=" S1 JUX B1201 " ideal model delta sigma weight residual 107.89 119.40 -11.51 3.00e+00 1.11e-01 1.47e+01 ... (remaining 10799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.85: 3974 15.85 - 31.70: 335 31.70 - 47.55: 110 47.55 - 63.39: 13 63.39 - 79.24: 6 Dihedral angle restraints: 4438 sinusoidal: 1338 harmonic: 3100 Sorted by residual: dihedral pdb=" CA CYS B 626 " pdb=" C CYS B 626 " pdb=" N LEU B 627 " pdb=" CA LEU B 627 " ideal model delta harmonic sigma weight residual 180.00 146.56 33.44 0 5.00e+00 4.00e-02 4.47e+01 dihedral pdb=" CA CYS A 626 " pdb=" C CYS A 626 " pdb=" N LEU A 627 " pdb=" CA LEU A 627 " ideal model delta harmonic sigma weight residual 180.00 146.63 33.37 0 5.00e+00 4.00e-02 4.45e+01 dihedral pdb=" CB CYS A 308 " pdb=" SG CYS A 308 " pdb=" SG CYS A 323 " pdb=" CB CYS A 323 " ideal model delta sinusoidal sigma weight residual -86.00 -133.74 47.74 1 1.00e+01 1.00e-02 3.14e+01 ... (remaining 4435 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1011 0.037 - 0.074: 276 0.074 - 0.111: 77 0.111 - 0.149: 12 0.149 - 0.186: 2 Chirality restraints: 1378 Sorted by residual: chirality pdb=" CA CYS B 626 " pdb=" N CYS B 626 " pdb=" C CYS B 626 " pdb=" CB CYS B 626 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.62e-01 chirality pdb=" CA CYS A 626 " pdb=" N CYS A 626 " pdb=" C CYS A 626 " pdb=" CB CYS A 626 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.19 2.00e-01 2.50e+01 8.57e-01 chirality pdb=" CA JUX A1201 " pdb=" N JUX A1201 " pdb=" C JUX A1201 " pdb=" C4 JUX A1201 " both_signs ideal model delta sigma weight residual True 2.59 -2.44 0.15 2.00e-01 2.50e+01 5.51e-01 ... (remaining 1375 not shown) Planarity restraints: 1332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N JUX B1201 " 0.122 2.00e-02 2.50e+03 9.89e-02 1.47e+02 pdb=" CA JUX B1201 " -0.138 2.00e-02 2.50e+03 pdb=" OH JUX B1201 " -0.131 2.00e-02 2.50e+03 pdb=" C1 JUX B1201 " 0.038 2.00e-02 2.50e+03 pdb=" C5 JUX B1201 " 0.042 2.00e-02 2.50e+03 pdb=" C9 JUX B1201 " 0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N JUX A1201 " -0.109 2.00e-02 2.50e+03 9.67e-02 1.40e+02 pdb=" CA JUX A1201 " 0.135 2.00e-02 2.50e+03 pdb=" OH JUX A1201 " 0.130 2.00e-02 2.50e+03 pdb=" C1 JUX A1201 " -0.033 2.00e-02 2.50e+03 pdb=" C5 JUX A1201 " -0.051 2.00e-02 2.50e+03 pdb=" C9 JUX A1201 " -0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 236 " -0.025 5.00e-02 4.00e+02 3.89e-02 2.43e+00 pdb=" N PRO A 237 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 237 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 237 " -0.022 5.00e-02 4.00e+02 ... (remaining 1329 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 63 2.57 - 3.15: 7567 3.15 - 3.74: 12592 3.74 - 4.32: 14991 4.32 - 4.90: 25341 Nonbonded interactions: 60554 Sorted by model distance: nonbonded pdb=" OH TYR B 292 " pdb=" OG SER B 468 " model vdw 1.990 2.440 nonbonded pdb=" OH TYR A 292 " pdb=" OG SER A 468 " model vdw 1.995 2.440 nonbonded pdb=" OG SER A 345 " pdb=" OD1 ASN A 347 " model vdw 1.997 2.440 nonbonded pdb=" OG SER B 345 " pdb=" OD1 ASN B 347 " model vdw 1.999 2.440 nonbonded pdb=" O6 NAG F 1 " pdb=" O5 NAG F 2 " model vdw 2.093 2.440 ... (remaining 60549 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.270 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 23.850 Find NCS groups from input model: 0.420 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6192 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.227 7852 Z= 0.416 Angle : 0.647 13.840 10804 Z= 0.285 Chirality : 0.038 0.186 1378 Planarity : 0.005 0.099 1328 Dihedral : 13.490 79.243 2436 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 50.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.28), residues: 1080 helix: 3.18 (0.21), residues: 626 sheet: None (None), residues: 0 loop : -1.75 (0.30), residues: 454 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 198 time to evaluate : 0.787 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 200 average time/residue: 0.1534 time to fit residues: 44.7474 Evaluate side-chains 127 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.915 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.0470 chunk 81 optimal weight: 7.9990 chunk 45 optimal weight: 0.0020 chunk 27 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 0.0060 chunk 84 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 overall best weight: 0.3302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 ASN B 250 ASN B 347 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6257 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 7852 Z= 0.225 Angle : 0.698 9.061 10804 Z= 0.335 Chirality : 0.045 0.213 1378 Planarity : 0.005 0.055 1328 Dihedral : 5.412 79.220 1136 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer Outliers : 4.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.27), residues: 1080 helix: 2.50 (0.21), residues: 626 sheet: None (None), residues: 0 loop : -1.69 (0.30), residues: 454 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 145 time to evaluate : 0.781 Fit side-chains outliers start: 29 outliers final: 18 residues processed: 163 average time/residue: 0.1539 time to fit residues: 36.2243 Evaluate side-chains 157 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 139 time to evaluate : 0.821 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.0714 time to fit residues: 3.4692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 81 optimal weight: 0.0670 chunk 66 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 97 optimal weight: 0.2980 chunk 33 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6277 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 7852 Z= 0.227 Angle : 0.641 9.266 10804 Z= 0.311 Chirality : 0.044 0.244 1378 Planarity : 0.005 0.051 1328 Dihedral : 5.571 80.020 1136 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer Outliers : 3.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.27), residues: 1080 helix: 2.27 (0.21), residues: 618 sheet: 2.35 (1.09), residues: 20 loop : -1.86 (0.30), residues: 442 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 146 time to evaluate : 0.722 Fit side-chains outliers start: 25 outliers final: 9 residues processed: 164 average time/residue: 0.1482 time to fit residues: 35.6330 Evaluate side-chains 149 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 140 time to evaluate : 0.773 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0742 time to fit residues: 2.3284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6320 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 7852 Z= 0.253 Angle : 0.645 9.434 10804 Z= 0.317 Chirality : 0.044 0.254 1378 Planarity : 0.005 0.053 1328 Dihedral : 5.635 79.479 1136 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer Outliers : 4.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.26), residues: 1080 helix: 2.13 (0.21), residues: 622 sheet: None (None), residues: 0 loop : -1.79 (0.29), residues: 458 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 143 time to evaluate : 0.851 Fit side-chains outliers start: 33 outliers final: 18 residues processed: 166 average time/residue: 0.1508 time to fit residues: 36.7538 Evaluate side-chains 149 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 131 time to evaluate : 0.880 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1076 time to fit residues: 4.3187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 77 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6344 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 7852 Z= 0.272 Angle : 0.662 9.434 10804 Z= 0.321 Chirality : 0.044 0.256 1378 Planarity : 0.005 0.056 1328 Dihedral : 5.720 79.289 1136 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer Outliers : 2.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.26), residues: 1080 helix: 2.11 (0.21), residues: 614 sheet: None (None), residues: 0 loop : -1.82 (0.28), residues: 466 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 130 time to evaluate : 0.824 Fit side-chains outliers start: 16 outliers final: 9 residues processed: 140 average time/residue: 0.1611 time to fit residues: 32.5670 Evaluate side-chains 135 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 126 time to evaluate : 0.821 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0743 time to fit residues: 2.3487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 20 optimal weight: 6.9990 chunk 61 optimal weight: 0.5980 chunk 25 optimal weight: 0.0970 chunk 104 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 7852 Z= 0.246 Angle : 0.653 9.414 10804 Z= 0.315 Chirality : 0.043 0.258 1378 Planarity : 0.005 0.058 1328 Dihedral : 5.684 79.160 1136 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer Outliers : 2.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.26), residues: 1080 helix: 2.08 (0.21), residues: 618 sheet: None (None), residues: 0 loop : -1.80 (0.29), residues: 462 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 130 time to evaluate : 0.796 Fit side-chains outliers start: 15 outliers final: 8 residues processed: 142 average time/residue: 0.1692 time to fit residues: 35.3609 Evaluate side-chains 132 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 124 time to evaluate : 0.828 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0781 time to fit residues: 2.3285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 76 optimal weight: 0.0270 chunk 87 optimal weight: 0.0050 chunk 58 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.4852 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 344 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6318 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 7852 Z= 0.208 Angle : 0.647 9.418 10804 Z= 0.308 Chirality : 0.043 0.250 1378 Planarity : 0.005 0.058 1328 Dihedral : 5.611 79.121 1136 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer Outliers : 1.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.27), residues: 1080 helix: 2.17 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -1.79 (0.29), residues: 464 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 128 time to evaluate : 0.883 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 141 average time/residue: 0.1652 time to fit residues: 33.9170 Evaluate side-chains 130 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 123 time to evaluate : 0.818 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0781 time to fit residues: 2.1107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 0.0370 chunk 20 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6335 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 7852 Z= 0.244 Angle : 0.660 9.446 10804 Z= 0.314 Chirality : 0.043 0.252 1378 Planarity : 0.005 0.058 1328 Dihedral : 5.621 79.041 1136 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer Outliers : 0.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.27), residues: 1080 helix: 2.13 (0.21), residues: 620 sheet: None (None), residues: 0 loop : -1.77 (0.29), residues: 460 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 124 time to evaluate : 0.825 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 130 average time/residue: 0.1461 time to fit residues: 28.2437 Evaluate side-chains 127 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 123 time to evaluate : 0.819 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0777 time to fit residues: 1.7436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.9990 chunk 97 optimal weight: 0.0870 chunk 99 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 29 optimal weight: 0.0040 chunk 87 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.6170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6324 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 7852 Z= 0.226 Angle : 0.656 9.433 10804 Z= 0.312 Chirality : 0.043 0.251 1378 Planarity : 0.005 0.058 1328 Dihedral : 5.605 79.178 1136 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.27), residues: 1080 helix: 2.18 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -1.80 (0.29), residues: 464 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 126 time to evaluate : 0.807 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 130 average time/residue: 0.1583 time to fit residues: 30.3084 Evaluate side-chains 126 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 120 time to evaluate : 0.858 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0731 time to fit residues: 1.9463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6388 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 7852 Z= 0.320 Angle : 0.704 9.472 10804 Z= 0.341 Chirality : 0.045 0.263 1378 Planarity : 0.005 0.059 1328 Dihedral : 5.856 80.354 1136 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer Outliers : 0.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.26), residues: 1080 helix: 1.99 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -1.82 (0.29), residues: 464 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 122 time to evaluate : 0.759 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 125 average time/residue: 0.1570 time to fit residues: 28.5192 Evaluate side-chains 118 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 115 time to evaluate : 0.747 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0745 time to fit residues: 1.4161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 23 optimal weight: 0.1980 chunk 85 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.177415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.150632 restraints weight = 9725.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.154008 restraints weight = 5684.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.156194 restraints weight = 4025.925| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 7852 Z= 0.237 Angle : 0.673 9.419 10804 Z= 0.321 Chirality : 0.043 0.253 1378 Planarity : 0.005 0.059 1328 Dihedral : 5.742 80.639 1136 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.27), residues: 1080 helix: 2.10 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -1.81 (0.29), residues: 464 =============================================================================== Job complete usr+sys time: 1581.20 seconds wall clock time: 29 minutes 28.83 seconds (1768.83 seconds total)