Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 20:27:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2o_23135/04_2023/7l2o_23135_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2o_23135/04_2023/7l2o_23135.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2o_23135/04_2023/7l2o_23135.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2o_23135/04_2023/7l2o_23135.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2o_23135/04_2023/7l2o_23135_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2o_23135/04_2023/7l2o_23135_updated.pdb" } resolution = 3.64 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= 0.004 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 96 5.16 5 C 10416 2.51 5 N 2492 2.21 5 O 2796 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 648": "OE1" <-> "OE2" Residue "A GLU 651": "OE1" <-> "OE2" Residue "A ASP 654": "OD1" <-> "OD2" Residue "C GLU 651": "OE1" <-> "OE2" Residue "C ASP 654": "OD1" <-> "OD2" Residue "D GLU 648": "OE1" <-> "OE2" Residue "D GLU 651": "OE1" <-> "OE2" Residue "D ASP 654": "OD1" <-> "OD2" Residue "B GLU 648": "OE1" <-> "OE2" Residue "B GLU 651": "OE1" <-> "OE2" Residue "B ASP 654": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 15800 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3904 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 466} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3904 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 466} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3904 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 466} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3904 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 466} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.60, per 1000 atoms: 0.54 Number of scatterers: 15800 At special positions: 0 Unit cell: (126.5, 125.35, 108.1, 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 96 16.00 O 2796 8.00 N 2492 7.00 C 10416 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 390 " distance=2.02 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 390 " distance=2.02 Simple disulfide: pdb=" SG CYS D 386 " - pdb=" SG CYS D 390 " distance=2.03 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 390 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.67 Conformation dependent library (CDL) restraints added in 2.2 seconds 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3648 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 82 helices and 4 sheets defined 59.0% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 251 through 258 Processing helix chain 'A' and resid 261 through 266 Processing helix chain 'A' and resid 287 through 293 removed outlier: 3.582A pdb=" N VAL A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 395 through 400 Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' Processing helix chain 'A' and resid 416 through 428 removed outlier: 4.357A pdb=" N LEU A 421 " --> pdb=" O PRO A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 453 Processing helix chain 'A' and resid 469 through 499 Processing helix chain 'A' and resid 505 through 508 No H-bonds generated for 'chain 'A' and resid 505 through 508' Processing helix chain 'A' and resid 511 through 531 Processing helix chain 'A' and resid 535 through 556 removed outlier: 3.661A pdb=" N VAL A 538 " --> pdb=" O LYS A 535 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL A 542 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N TRP A 549 " --> pdb=" O ALA A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 575 removed outlier: 4.597A pdb=" N TYR A 565 " --> pdb=" O GLN A 561 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N MET A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE A 569 " --> pdb=" O TYR A 565 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU A 570 " --> pdb=" O ALA A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 598 removed outlier: 3.692A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 641 removed outlier: 3.995A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N THR A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 670 Processing helix chain 'A' and resid 674 through 689 Processing helix chain 'A' and resid 692 through 711 Processing helix chain 'C' and resid 251 through 258 Processing helix chain 'C' and resid 261 through 268 Processing helix chain 'C' and resid 287 through 293 Processing helix chain 'C' and resid 299 through 319 Processing helix chain 'C' and resid 336 through 343 Processing helix chain 'C' and resid 346 through 352 Processing helix chain 'C' and resid 363 through 365 No H-bonds generated for 'chain 'C' and resid 363 through 365' Processing helix chain 'C' and resid 395 through 400 Processing helix chain 'C' and resid 412 through 414 No H-bonds generated for 'chain 'C' and resid 412 through 414' Processing helix chain 'C' and resid 416 through 428 removed outlier: 4.312A pdb=" N LEU C 421 " --> pdb=" O PRO C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 453 Processing helix chain 'C' and resid 469 through 499 Processing helix chain 'C' and resid 505 through 508 No H-bonds generated for 'chain 'C' and resid 505 through 508' Processing helix chain 'C' and resid 511 through 531 Processing helix chain 'C' and resid 535 through 556 removed outlier: 3.683A pdb=" N VAL C 538 " --> pdb=" O LYS C 535 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL C 542 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA C 546 " --> pdb=" O PHE C 543 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TRP C 549 " --> pdb=" O ALA C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 575 removed outlier: 4.688A pdb=" N TYR C 565 " --> pdb=" O GLN C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 598 removed outlier: 3.914A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 641 removed outlier: 3.991A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N THR C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 670 Processing helix chain 'C' and resid 674 through 689 Processing helix chain 'C' and resid 692 through 711 Processing helix chain 'D' and resid 251 through 258 Processing helix chain 'D' and resid 261 through 268 Processing helix chain 'D' and resid 287 through 293 removed outlier: 3.647A pdb=" N VAL D 292 " --> pdb=" O LEU D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 319 Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'D' and resid 346 through 352 Processing helix chain 'D' and resid 363 through 365 No H-bonds generated for 'chain 'D' and resid 363 through 365' Processing helix chain 'D' and resid 395 through 400 Processing helix chain 'D' and resid 412 through 414 No H-bonds generated for 'chain 'D' and resid 412 through 414' Processing helix chain 'D' and resid 416 through 428 removed outlier: 3.963A pdb=" N LEU D 421 " --> pdb=" O PRO D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 453 Processing helix chain 'D' and resid 469 through 499 Processing helix chain 'D' and resid 511 through 531 Processing helix chain 'D' and resid 535 through 556 removed outlier: 3.645A pdb=" N VAL D 538 " --> pdb=" O LYS D 535 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL D 542 " --> pdb=" O ALA D 539 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TRP D 549 " --> pdb=" O ALA D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 575 removed outlier: 4.911A pdb=" N TYR D 565 " --> pdb=" O GLN D 561 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET D 568 " --> pdb=" O ILE D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 598 Processing helix chain 'D' and resid 630 through 641 removed outlier: 4.010A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N THR D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 670 Processing helix chain 'D' and resid 674 through 689 Processing helix chain 'D' and resid 692 through 711 Processing helix chain 'B' and resid 251 through 258 Processing helix chain 'B' and resid 262 through 268 Processing helix chain 'B' and resid 287 through 293 Processing helix chain 'B' and resid 299 through 319 Processing helix chain 'B' and resid 336 through 343 Processing helix chain 'B' and resid 346 through 352 Processing helix chain 'B' and resid 363 through 365 No H-bonds generated for 'chain 'B' and resid 363 through 365' Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 416 through 428 removed outlier: 4.136A pdb=" N LEU B 421 " --> pdb=" O PRO B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 453 Processing helix chain 'B' and resid 469 through 499 Processing helix chain 'B' and resid 511 through 531 Processing helix chain 'B' and resid 536 through 556 removed outlier: 4.040A pdb=" N VAL B 542 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE B 543 " --> pdb=" O SER B 540 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N TRP B 549 " --> pdb=" O ALA B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 575 removed outlier: 4.762A pdb=" N TYR B 565 " --> pdb=" O GLN B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 598 Processing helix chain 'B' and resid 630 through 640 removed outlier: 4.048A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 670 Processing helix chain 'B' and resid 674 through 688 Processing helix chain 'B' and resid 692 through 711 Processing sheet with id= A, first strand: chain 'A' and resid 742 through 745 removed outlier: 3.736A pdb=" N TRP A 372 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU A 381 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N THR A 370 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 742 through 745 removed outlier: 6.448A pdb=" N LEU C 381 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N THR C 370 " --> pdb=" O LEU C 381 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 742 through 745 removed outlier: 6.471A pdb=" N LEU D 381 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N THR D 370 " --> pdb=" O LEU D 381 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 742 through 746 removed outlier: 3.680A pdb=" N TRP B 372 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU B 381 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N THR B 370 " --> pdb=" O LEU B 381 " (cutoff:3.500A) 805 hydrogen bonds defined for protein. 2214 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: 4.13 Time building geometry restraints manager: 7.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3839 1.33 - 1.45: 3619 1.45 - 1.57: 8590 1.57 - 1.70: 0 1.70 - 1.82: 156 Bond restraints: 16204 Sorted by residual: bond pdb=" CBK 6EU D 901 " pdb=" OAF 6EU D 901 " ideal model delta sigma weight residual 1.329 1.448 -0.119 2.00e-02 2.50e+03 3.57e+01 bond pdb=" CBK 6EU C 901 " pdb=" OAF 6EU C 901 " ideal model delta sigma weight residual 1.329 1.448 -0.119 2.00e-02 2.50e+03 3.57e+01 bond pdb=" CBK 6EU A 901 " pdb=" OAF 6EU A 901 " ideal model delta sigma weight residual 1.329 1.448 -0.119 2.00e-02 2.50e+03 3.54e+01 bond pdb=" CBK 6EU B 901 " pdb=" OAF 6EU B 901 " ideal model delta sigma weight residual 1.329 1.448 -0.119 2.00e-02 2.50e+03 3.53e+01 bond pdb=" C PHE D 649 " pdb=" N THR D 650 " ideal model delta sigma weight residual 1.331 1.363 -0.032 1.29e-02 6.01e+03 5.97e+00 ... (remaining 16199 not shown) Histogram of bond angle deviations from ideal: 97.29 - 104.64: 231 104.64 - 112.00: 7690 112.00 - 119.35: 5773 119.35 - 126.70: 8122 126.70 - 134.05: 168 Bond angle restraints: 21984 Sorted by residual: angle pdb=" C SER A 711 " pdb=" N PHE A 712 " pdb=" CA PHE A 712 " ideal model delta sigma weight residual 121.54 129.25 -7.71 1.91e+00 2.74e-01 1.63e+01 angle pdb=" C SER C 711 " pdb=" N PHE C 712 " pdb=" CA PHE C 712 " ideal model delta sigma weight residual 121.54 129.25 -7.71 1.91e+00 2.74e-01 1.63e+01 angle pdb=" C SER B 711 " pdb=" N PHE B 712 " pdb=" CA PHE B 712 " ideal model delta sigma weight residual 121.54 129.21 -7.67 1.91e+00 2.74e-01 1.61e+01 angle pdb=" C SER D 711 " pdb=" N PHE D 712 " pdb=" CA PHE D 712 " ideal model delta sigma weight residual 121.54 129.20 -7.66 1.91e+00 2.74e-01 1.61e+01 angle pdb=" N ASP A 654 " pdb=" CA ASP A 654 " pdb=" C ASP A 654 " ideal model delta sigma weight residual 110.53 115.72 -5.19 1.32e+00 5.74e-01 1.55e+01 ... (remaining 21979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 8658 17.44 - 34.89: 663 34.89 - 52.33: 119 52.33 - 69.77: 19 69.77 - 87.22: 9 Dihedral angle restraints: 9468 sinusoidal: 3796 harmonic: 5672 Sorted by residual: dihedral pdb=" CA PHE C 712 " pdb=" C PHE C 712 " pdb=" N LEU C 713 " pdb=" CA LEU C 713 " ideal model delta harmonic sigma weight residual 180.00 153.36 26.64 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA PHE D 712 " pdb=" C PHE D 712 " pdb=" N LEU D 713 " pdb=" CA LEU D 713 " ideal model delta harmonic sigma weight residual 180.00 153.98 26.02 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA PHE A 712 " pdb=" C PHE A 712 " pdb=" N LEU A 713 " pdb=" CA LEU A 713 " ideal model delta harmonic sigma weight residual 180.00 154.82 25.18 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 9465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1947 0.057 - 0.115: 468 0.115 - 0.172: 53 0.172 - 0.230: 4 0.230 - 0.287: 4 Chirality restraints: 2476 Sorted by residual: chirality pdb=" CA ASN A 652 " pdb=" N ASN A 652 " pdb=" C ASN A 652 " pdb=" CB ASN A 652 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA ASN B 652 " pdb=" N ASN B 652 " pdb=" C ASN B 652 " pdb=" CB ASN B 652 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA ASN C 652 " pdb=" N ASN C 652 " pdb=" C ASN C 652 " pdb=" CB ASN C 652 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.03e+00 ... (remaining 2473 not shown) Planarity restraints: 2692 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY D 548 " 0.014 2.00e-02 2.50e+03 2.73e-02 7.48e+00 pdb=" C GLY D 548 " -0.047 2.00e-02 2.50e+03 pdb=" O GLY D 548 " 0.018 2.00e-02 2.50e+03 pdb=" N TRP D 549 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 548 " 0.013 2.00e-02 2.50e+03 2.64e-02 6.98e+00 pdb=" C GLY A 548 " -0.046 2.00e-02 2.50e+03 pdb=" O GLY A 548 " 0.017 2.00e-02 2.50e+03 pdb=" N TRP A 549 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 548 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.86e+00 pdb=" C GLY B 548 " 0.045 2.00e-02 2.50e+03 pdb=" O GLY B 548 " -0.017 2.00e-02 2.50e+03 pdb=" N TRP B 549 " -0.015 2.00e-02 2.50e+03 ... (remaining 2689 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 163 2.57 - 3.15: 13798 3.15 - 3.74: 23715 3.74 - 4.32: 32020 4.32 - 4.90: 53649 Nonbonded interactions: 123345 Sorted by model distance: nonbonded pdb=" OH TYR D 495 " pdb=" OG SER D 510 " model vdw 1.989 2.440 nonbonded pdb=" OH TYR B 495 " pdb=" OG SER B 510 " model vdw 2.022 2.440 nonbonded pdb=" O LEU A 384 " pdb=" NH2 ARG A 721 " model vdw 2.130 2.520 nonbonded pdb=" OG SER A 379 " pdb=" OD1 ASP A 745 " model vdw 2.139 2.440 nonbonded pdb=" OH TYR A 495 " pdb=" OG SER A 510 " model vdw 2.140 2.440 ... (remaining 123340 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' selection = chain 'C' selection = chain 'D' } 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: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.980 Check model and map are aligned: 0.240 Set scattering table: 0.130 Process input model: 40.760 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.070 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 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 : 0.010 0.119 16204 Z= 0.626 Angle : 0.892 9.360 21984 Z= 0.483 Chirality : 0.050 0.287 2476 Planarity : 0.004 0.028 2692 Dihedral : 12.842 87.217 5808 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer Outliers : 1.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.84 (0.18), residues: 1904 helix: 0.49 (0.14), residues: 1184 sheet: -4.24 (0.61), residues: 40 loop : -2.20 (0.21), residues: 680 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 620 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 10 residues processed: 634 average time/residue: 0.3155 time to fit residues: 279.4296 Evaluate side-chains 441 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 431 time to evaluate : 1.931 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1343 time to fit residues: 5.2028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.9980 chunk 145 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 150 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 112 optimal weight: 10.0000 chunk 174 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 GLN B 560 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 16204 Z= 0.179 Angle : 0.591 9.034 21984 Z= 0.306 Chirality : 0.039 0.157 2476 Planarity : 0.003 0.024 2692 Dihedral : 5.164 58.187 2144 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer Outliers : 1.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.41 (0.19), residues: 1904 helix: 1.66 (0.15), residues: 1144 sheet: -2.76 (0.66), residues: 60 loop : -1.87 (0.23), residues: 700 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 500 time to evaluate : 1.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 10 residues processed: 514 average time/residue: 0.2780 time to fit residues: 208.2106 Evaluate side-chains 438 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 428 time to evaluate : 1.880 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1347 time to fit residues: 5.1664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 0.0770 chunk 54 optimal weight: 0.9990 chunk 145 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 chunk 48 optimal weight: 20.0000 chunk 174 optimal weight: 0.8980 chunk 188 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 173 optimal weight: 0.6980 chunk 59 optimal weight: 8.9990 chunk 140 optimal weight: 10.0000 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 ASN C 551 ASN D 354 GLN B 551 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 16204 Z= 0.156 Angle : 0.555 12.327 21984 Z= 0.281 Chirality : 0.038 0.172 2476 Planarity : 0.003 0.055 2692 Dihedral : 4.945 58.309 2144 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer Outliers : 2.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.72 (0.20), residues: 1904 helix: 1.91 (0.15), residues: 1120 sheet: -2.64 (0.66), residues: 60 loop : -1.64 (0.23), residues: 724 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 471 time to evaluate : 1.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 22 residues processed: 481 average time/residue: 0.2898 time to fit residues: 203.0701 Evaluate side-chains 438 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 416 time to evaluate : 1.977 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1749 time to fit residues: 9.1796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 117 optimal weight: 0.0870 chunk 175 optimal weight: 2.9990 chunk 185 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 166 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 551 ASN ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 16204 Z= 0.226 Angle : 0.596 11.466 21984 Z= 0.302 Chirality : 0.040 0.168 2476 Planarity : 0.003 0.041 2692 Dihedral : 4.955 59.935 2144 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer Outliers : 2.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.48 (0.20), residues: 1904 helix: 1.65 (0.15), residues: 1148 sheet: -2.63 (0.66), residues: 60 loop : -1.74 (0.23), residues: 696 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 451 time to evaluate : 1.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 21 residues processed: 466 average time/residue: 0.2880 time to fit residues: 194.8481 Evaluate side-chains 443 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 422 time to evaluate : 1.863 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1601 time to fit residues: 8.6666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 138 optimal weight: 10.0000 chunk 76 optimal weight: 0.8980 chunk 158 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 chunk 166 optimal weight: 4.9990 chunk 46 optimal weight: 0.0670 overall best weight: 1.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 ASN C 320 HIS C 551 ASN B 354 GLN B 551 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 16204 Z= 0.242 Angle : 0.601 11.626 21984 Z= 0.303 Chirality : 0.040 0.176 2476 Planarity : 0.003 0.043 2692 Dihedral : 4.948 58.045 2144 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer Outliers : 1.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.43 (0.20), residues: 1904 helix: 1.61 (0.15), residues: 1144 sheet: -2.64 (0.66), residues: 60 loop : -1.75 (0.23), residues: 700 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 435 time to evaluate : 1.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 17 residues processed: 448 average time/residue: 0.2910 time to fit residues: 190.3497 Evaluate side-chains 427 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 410 time to evaluate : 2.009 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1598 time to fit residues: 7.2091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 0.6980 chunk 167 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 185 optimal weight: 0.9990 chunk 154 optimal weight: 8.9990 chunk 86 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 ASN C 551 ASN D 551 ASN B 354 GLN B 551 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 16204 Z= 0.164 Angle : 0.573 11.610 21984 Z= 0.293 Chirality : 0.039 0.218 2476 Planarity : 0.003 0.048 2692 Dihedral : 4.867 58.224 2144 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.64 (0.20), residues: 1904 helix: 1.85 (0.15), residues: 1120 sheet: -2.51 (0.68), residues: 60 loop : -1.68 (0.22), residues: 724 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 447 time to evaluate : 1.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 453 average time/residue: 0.2833 time to fit residues: 187.5542 Evaluate side-chains 416 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 409 time to evaluate : 2.204 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1586 time to fit residues: 4.7809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 105 optimal weight: 10.0000 chunk 135 optimal weight: 0.9980 chunk 156 optimal weight: 6.9990 chunk 103 optimal weight: 0.0000 chunk 185 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 85 optimal weight: 0.0970 chunk 114 optimal weight: 0.6980 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 ASN C 551 ASN ** C 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.4468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 16204 Z= 0.152 Angle : 0.575 11.892 21984 Z= 0.290 Chirality : 0.040 0.209 2476 Planarity : 0.003 0.043 2692 Dihedral : 4.828 59.148 2144 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.71 (0.20), residues: 1904 helix: 1.91 (0.15), residues: 1120 sheet: -2.41 (0.70), residues: 60 loop : -1.67 (0.23), residues: 724 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 431 time to evaluate : 1.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 17 residues processed: 438 average time/residue: 0.2685 time to fit residues: 173.8085 Evaluate side-chains 421 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 404 time to evaluate : 1.703 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1415 time to fit residues: 6.8547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 55 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 126 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 145 optimal weight: 9.9990 chunk 168 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 320 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 16204 Z= 0.213 Angle : 0.624 11.501 21984 Z= 0.318 Chirality : 0.041 0.198 2476 Planarity : 0.003 0.043 2692 Dihedral : 4.866 58.854 2144 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.43 (0.20), residues: 1904 helix: 1.59 (0.15), residues: 1148 sheet: -2.37 (0.70), residues: 60 loop : -1.76 (0.23), residues: 696 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 433 time to evaluate : 1.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 433 average time/residue: 0.2911 time to fit residues: 185.7099 Evaluate side-chains 424 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 419 time to evaluate : 1.794 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1483 time to fit residues: 3.9096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 2.9990 chunk 161 optimal weight: 0.0270 chunk 172 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 155 optimal weight: 10.0000 chunk 163 optimal weight: 0.9990 chunk 171 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.4676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 16204 Z= 0.174 Angle : 0.606 12.031 21984 Z= 0.308 Chirality : 0.040 0.216 2476 Planarity : 0.003 0.043 2692 Dihedral : 4.851 59.058 2144 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.49 (0.20), residues: 1904 helix: 1.65 (0.15), residues: 1148 sheet: -2.24 (0.71), residues: 60 loop : -1.78 (0.23), residues: 696 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 425 time to evaluate : 1.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 426 average time/residue: 0.2756 time to fit residues: 173.8304 Evaluate side-chains 413 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 405 time to evaluate : 1.885 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1536 time to fit residues: 4.9395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 chunk 86 optimal weight: 0.0070 chunk 126 optimal weight: 0.5980 chunk 191 optimal weight: 0.7980 chunk 176 optimal weight: 0.9990 chunk 152 optimal weight: 0.2980 chunk 15 optimal weight: 6.9990 chunk 117 optimal weight: 0.0980 chunk 93 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 overall best weight: 0.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 270 ASN C 533 GLN C 551 ASN ** C 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.4928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.070 16204 Z= 0.171 Angle : 0.658 13.003 21984 Z= 0.335 Chirality : 0.040 0.195 2476 Planarity : 0.003 0.044 2692 Dihedral : 4.839 59.890 2144 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.53 (0.20), residues: 1904 helix: 1.72 (0.16), residues: 1136 sheet: -2.08 (0.71), residues: 60 loop : -1.79 (0.23), residues: 708 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 430 time to evaluate : 1.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 431 average time/residue: 0.2705 time to fit residues: 173.5540 Evaluate side-chains 417 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 413 time to evaluate : 1.759 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1443 time to fit residues: 3.5226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 152 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 156 optimal weight: 8.9990 chunk 19 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 133 optimal weight: 0.5980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 GLN ** 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 = 0.4252 r_free = 0.4252 target = 0.199528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.126149 restraints weight = 22317.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.130241 restraints weight = 11221.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.132630 restraints weight = 7878.120| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.4940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 16204 Z= 0.218 Angle : 0.668 13.590 21984 Z= 0.339 Chirality : 0.042 0.208 2476 Planarity : 0.003 0.044 2692 Dihedral : 4.863 59.668 2144 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.44 (0.20), residues: 1904 helix: 1.58 (0.15), residues: 1148 sheet: -2.00 (0.71), residues: 60 loop : -1.77 (0.23), residues: 696 =============================================================================== Job complete usr+sys time: 3783.38 seconds wall clock time: 69 minutes 4.30 seconds (4144.30 seconds total)