Starting phenix.real_space_refine (version: dev) on Mon Apr 4 18:24:02 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yrn_6842/04_2022/5yrn_6842.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yrn_6842/04_2022/5yrn_6842.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yrn_6842/04_2022/5yrn_6842.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yrn_6842/04_2022/5yrn_6842.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yrn_6842/04_2022/5yrn_6842.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yrn_6842/04_2022/5yrn_6842.pdb" } resolution = 4.1 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= 0.001 sd= 0.005 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 8280 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 690 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "B" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 690 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "C" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 690 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "D" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 690 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "E" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 690 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "F" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 690 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "G" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 690 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "H" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 690 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "I" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 690 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "J" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 690 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "K" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 690 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "L" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 690 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Time building chain proxies: 5.11, per 1000 atoms: 0.62 Number of scatterers: 8280 At special positions: 0 Unit cell: (89.79, 89.79, 95.94, 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 48 16.00 O 1680 8.00 N 1452 7.00 C 5100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.37 Conformation dependent library (CDL) restraints added in 1.1 seconds 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2016 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 0 sheets defined 87.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 430 through 443 removed outlier: 3.773A pdb=" N GLN A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 451 Processing helix chain 'A' and resid 452 through 466 removed outlier: 3.573A pdb=" N SER A 459 " --> pdb=" O CYS A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 479 Processing helix chain 'A' and resid 482 through 497 removed outlier: 3.523A pdb=" N GLN A 489 " --> pdb=" O SER A 485 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 490 " --> pdb=" O LYS A 486 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE A 496 " --> pdb=" O ASP A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 512 removed outlier: 3.773A pdb=" N VAL A 504 " --> pdb=" O GLU A 500 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE A 505 " --> pdb=" O PHE A 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 443 removed outlier: 3.772A pdb=" N GLN B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 451 Processing helix chain 'B' and resid 452 through 466 removed outlier: 3.574A pdb=" N SER B 459 " --> pdb=" O CYS B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 479 Processing helix chain 'B' and resid 482 through 497 removed outlier: 3.522A pdb=" N GLN B 489 " --> pdb=" O SER B 485 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU B 490 " --> pdb=" O LYS B 486 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE B 496 " --> pdb=" O ASP B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 512 removed outlier: 3.774A pdb=" N VAL B 504 " --> pdb=" O GLU B 500 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ILE B 505 " --> pdb=" O PHE B 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 443 removed outlier: 3.773A pdb=" N GLN C 437 " --> pdb=" O ALA C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 451 Processing helix chain 'C' and resid 452 through 466 removed outlier: 3.573A pdb=" N SER C 459 " --> pdb=" O CYS C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 479 Processing helix chain 'C' and resid 482 through 497 removed outlier: 3.523A pdb=" N GLN C 489 " --> pdb=" O SER C 485 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU C 490 " --> pdb=" O LYS C 486 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE C 496 " --> pdb=" O ASP C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 512 removed outlier: 3.773A pdb=" N VAL C 504 " --> pdb=" O GLU C 500 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE C 505 " --> pdb=" O PHE C 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 443 removed outlier: 3.772A pdb=" N GLN D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 451 Processing helix chain 'D' and resid 452 through 466 removed outlier: 3.573A pdb=" N SER D 459 " --> pdb=" O CYS D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 479 Processing helix chain 'D' and resid 482 through 497 removed outlier: 3.522A pdb=" N GLN D 489 " --> pdb=" O SER D 485 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU D 490 " --> pdb=" O LYS D 486 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE D 496 " --> pdb=" O ASP D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 512 removed outlier: 3.773A pdb=" N VAL D 504 " --> pdb=" O GLU D 500 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ILE D 505 " --> pdb=" O PHE D 501 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 443 removed outlier: 3.773A pdb=" N GLN E 437 " --> pdb=" O ALA E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 444 through 451 Processing helix chain 'E' and resid 452 through 466 removed outlier: 3.573A pdb=" N SER E 459 " --> pdb=" O CYS E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 479 Processing helix chain 'E' and resid 482 through 497 removed outlier: 3.523A pdb=" N GLN E 489 " --> pdb=" O SER E 485 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU E 490 " --> pdb=" O LYS E 486 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP E 495 " --> pdb=" O LEU E 491 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE E 496 " --> pdb=" O ASP E 492 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 512 removed outlier: 3.773A pdb=" N VAL E 504 " --> pdb=" O GLU E 500 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE E 505 " --> pdb=" O PHE E 501 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 443 removed outlier: 3.773A pdb=" N GLN F 437 " --> pdb=" O ALA F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 444 through 451 Processing helix chain 'F' and resid 452 through 466 removed outlier: 3.573A pdb=" N SER F 459 " --> pdb=" O CYS F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 470 through 479 Processing helix chain 'F' and resid 482 through 497 removed outlier: 3.523A pdb=" N GLN F 489 " --> pdb=" O SER F 485 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU F 490 " --> pdb=" O LYS F 486 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP F 495 " --> pdb=" O LEU F 491 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE F 496 " --> pdb=" O ASP F 492 " (cutoff:3.500A) Processing helix chain 'F' and resid 499 through 512 removed outlier: 3.774A pdb=" N VAL F 504 " --> pdb=" O GLU F 500 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE F 505 " --> pdb=" O PHE F 501 " (cutoff:3.500A) Processing helix chain 'G' and resid 431 through 443 removed outlier: 3.772A pdb=" N GLN G 437 " --> pdb=" O ALA G 433 " (cutoff:3.500A) Processing helix chain 'G' and resid 444 through 451 Processing helix chain 'G' and resid 452 through 466 removed outlier: 3.574A pdb=" N SER G 459 " --> pdb=" O CYS G 455 " (cutoff:3.500A) Processing helix chain 'G' and resid 470 through 479 Processing helix chain 'G' and resid 482 through 497 removed outlier: 3.523A pdb=" N GLN G 489 " --> pdb=" O SER G 485 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU G 490 " --> pdb=" O LYS G 486 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP G 495 " --> pdb=" O LEU G 491 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE G 496 " --> pdb=" O ASP G 492 " (cutoff:3.500A) Processing helix chain 'G' and resid 499 through 512 removed outlier: 3.774A pdb=" N VAL G 504 " --> pdb=" O GLU G 500 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE G 505 " --> pdb=" O PHE G 501 " (cutoff:3.500A) Processing helix chain 'H' and resid 431 through 443 removed outlier: 3.773A pdb=" N GLN H 437 " --> pdb=" O ALA H 433 " (cutoff:3.500A) Processing helix chain 'H' and resid 444 through 451 Processing helix chain 'H' and resid 452 through 466 removed outlier: 3.573A pdb=" N SER H 459 " --> pdb=" O CYS H 455 " (cutoff:3.500A) Processing helix chain 'H' and resid 470 through 479 Processing helix chain 'H' and resid 482 through 497 removed outlier: 3.522A pdb=" N GLN H 489 " --> pdb=" O SER H 485 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU H 490 " --> pdb=" O LYS H 486 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP H 495 " --> pdb=" O LEU H 491 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE H 496 " --> pdb=" O ASP H 492 " (cutoff:3.500A) Processing helix chain 'H' and resid 499 through 512 removed outlier: 3.773A pdb=" N VAL H 504 " --> pdb=" O GLU H 500 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE H 505 " --> pdb=" O PHE H 501 " (cutoff:3.500A) Processing helix chain 'I' and resid 431 through 443 removed outlier: 3.773A pdb=" N GLN I 437 " --> pdb=" O ALA I 433 " (cutoff:3.500A) Processing helix chain 'I' and resid 444 through 451 Processing helix chain 'I' and resid 452 through 466 removed outlier: 3.573A pdb=" N SER I 459 " --> pdb=" O CYS I 455 " (cutoff:3.500A) Processing helix chain 'I' and resid 470 through 479 Processing helix chain 'I' and resid 482 through 497 removed outlier: 3.523A pdb=" N GLN I 489 " --> pdb=" O SER I 485 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU I 490 " --> pdb=" O LYS I 486 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP I 495 " --> pdb=" O LEU I 491 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE I 496 " --> pdb=" O ASP I 492 " (cutoff:3.500A) Processing helix chain 'I' and resid 499 through 512 removed outlier: 3.774A pdb=" N VAL I 504 " --> pdb=" O GLU I 500 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE I 505 " --> pdb=" O PHE I 501 " (cutoff:3.500A) Processing helix chain 'J' and resid 431 through 443 removed outlier: 3.772A pdb=" N GLN J 437 " --> pdb=" O ALA J 433 " (cutoff:3.500A) Processing helix chain 'J' and resid 444 through 451 Processing helix chain 'J' and resid 452 through 466 removed outlier: 3.574A pdb=" N SER J 459 " --> pdb=" O CYS J 455 " (cutoff:3.500A) Processing helix chain 'J' and resid 470 through 479 Processing helix chain 'J' and resid 482 through 497 removed outlier: 3.523A pdb=" N GLN J 489 " --> pdb=" O SER J 485 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU J 490 " --> pdb=" O LYS J 486 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP J 495 " --> pdb=" O LEU J 491 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE J 496 " --> pdb=" O ASP J 492 " (cutoff:3.500A) Processing helix chain 'J' and resid 499 through 512 removed outlier: 3.773A pdb=" N VAL J 504 " --> pdb=" O GLU J 500 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE J 505 " --> pdb=" O PHE J 501 " (cutoff:3.500A) Processing helix chain 'K' and resid 431 through 443 removed outlier: 3.772A pdb=" N GLN K 437 " --> pdb=" O ALA K 433 " (cutoff:3.500A) Processing helix chain 'K' and resid 444 through 451 Processing helix chain 'K' and resid 452 through 466 removed outlier: 3.573A pdb=" N SER K 459 " --> pdb=" O CYS K 455 " (cutoff:3.500A) Processing helix chain 'K' and resid 470 through 479 Processing helix chain 'K' and resid 482 through 497 removed outlier: 3.522A pdb=" N GLN K 489 " --> pdb=" O SER K 485 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU K 490 " --> pdb=" O LYS K 486 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP K 495 " --> pdb=" O LEU K 491 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE K 496 " --> pdb=" O ASP K 492 " (cutoff:3.500A) Processing helix chain 'K' and resid 499 through 512 removed outlier: 3.773A pdb=" N VAL K 504 " --> pdb=" O GLU K 500 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE K 505 " --> pdb=" O PHE K 501 " (cutoff:3.500A) Processing helix chain 'L' and resid 431 through 443 removed outlier: 3.773A pdb=" N GLN L 437 " --> pdb=" O ALA L 433 " (cutoff:3.500A) Processing helix chain 'L' and resid 444 through 451 Processing helix chain 'L' and resid 452 through 466 removed outlier: 3.573A pdb=" N SER L 459 " --> pdb=" O CYS L 455 " (cutoff:3.500A) Processing helix chain 'L' and resid 470 through 479 Processing helix chain 'L' and resid 482 through 497 removed outlier: 3.522A pdb=" N GLN L 489 " --> pdb=" O SER L 485 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU L 490 " --> pdb=" O LYS L 486 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP L 495 " --> pdb=" O LEU L 491 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE L 496 " --> pdb=" O ASP L 492 " (cutoff:3.500A) Processing helix chain 'L' and resid 499 through 512 removed outlier: 3.773A pdb=" N VAL L 504 " --> pdb=" O GLU L 500 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE L 505 " --> pdb=" O PHE L 501 " (cutoff:3.500A) 529 hydrogen bonds defined for protein. 1587 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: 2.19 Time building geometry restraints manager: 3.60 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: 2681 1.34 - 1.45: 809 1.45 - 1.57: 4754 1.57 - 1.69: 0 1.69 - 1.80: 84 Bond restraints: 8328 Sorted by residual: bond pdb=" N LYS G 443 " pdb=" CA LYS G 443 " ideal model delta sigma weight residual 1.463 1.437 0.026 1.36e-02 5.41e+03 3.56e+00 bond pdb=" N LYS L 443 " pdb=" CA LYS L 443 " ideal model delta sigma weight residual 1.463 1.438 0.025 1.36e-02 5.41e+03 3.49e+00 bond pdb=" N LYS D 443 " pdb=" CA LYS D 443 " ideal model delta sigma weight residual 1.463 1.438 0.025 1.36e-02 5.41e+03 3.41e+00 bond pdb=" N LYS C 443 " pdb=" CA LYS C 443 " ideal model delta sigma weight residual 1.463 1.438 0.025 1.36e-02 5.41e+03 3.40e+00 bond pdb=" N LYS H 443 " pdb=" CA LYS H 443 " ideal model delta sigma weight residual 1.463 1.438 0.025 1.36e-02 5.41e+03 3.37e+00 ... (remaining 8323 not shown) Histogram of bond angle deviations from ideal: 100.33 - 107.04: 148 107.04 - 113.74: 5019 113.74 - 120.45: 3096 120.45 - 127.16: 2885 127.16 - 133.87: 36 Bond angle restraints: 11184 Sorted by residual: angle pdb=" C GLN J 514 " pdb=" N MET J 515 " pdb=" CA MET J 515 " ideal model delta sigma weight residual 122.40 126.32 -3.92 1.45e+00 4.76e-01 7.29e+00 angle pdb=" C GLN H 514 " pdb=" N MET H 515 " pdb=" CA MET H 515 " ideal model delta sigma weight residual 122.40 126.30 -3.90 1.45e+00 4.76e-01 7.25e+00 angle pdb=" C GLN E 514 " pdb=" N MET E 515 " pdb=" CA MET E 515 " ideal model delta sigma weight residual 122.40 126.30 -3.90 1.45e+00 4.76e-01 7.24e+00 angle pdb=" C GLN C 514 " pdb=" N MET C 515 " pdb=" CA MET C 515 " ideal model delta sigma weight residual 122.40 126.30 -3.90 1.45e+00 4.76e-01 7.24e+00 angle pdb=" C GLN B 514 " pdb=" N MET B 515 " pdb=" CA MET B 515 " ideal model delta sigma weight residual 122.40 126.30 -3.90 1.45e+00 4.76e-01 7.22e+00 ... (remaining 11179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.42: 4919 13.42 - 26.83: 265 26.83 - 40.25: 60 40.25 - 53.66: 36 53.66 - 67.08: 12 Dihedral angle restraints: 5292 sinusoidal: 2232 harmonic: 3060 Sorted by residual: dihedral pdb=" CA LEU D 456 " pdb=" C LEU D 456 " pdb=" N ASN D 457 " pdb=" CA ASN D 457 " ideal model delta harmonic sigma weight residual -180.00 -159.85 -20.15 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA LEU H 456 " pdb=" C LEU H 456 " pdb=" N ASN H 457 " pdb=" CA ASN H 457 " ideal model delta harmonic sigma weight residual 180.00 -159.88 -20.12 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA LEU A 456 " pdb=" C LEU A 456 " pdb=" N ASN A 457 " pdb=" CA ASN A 457 " ideal model delta harmonic sigma weight residual 180.00 -159.88 -20.12 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 5289 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 848 0.040 - 0.080: 340 0.080 - 0.120: 108 0.120 - 0.160: 24 0.160 - 0.199: 12 Chirality restraints: 1332 Sorted by residual: chirality pdb=" CB ILE L 469 " pdb=" CA ILE L 469 " pdb=" CG1 ILE L 469 " pdb=" CG2 ILE L 469 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.95e-01 chirality pdb=" CB ILE B 469 " pdb=" CA ILE B 469 " pdb=" CG1 ILE B 469 " pdb=" CG2 ILE B 469 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.86e-01 chirality pdb=" CB ILE H 469 " pdb=" CA ILE H 469 " pdb=" CG1 ILE H 469 " pdb=" CG2 ILE H 469 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.84e-01 ... (remaining 1329 not shown) Planarity restraints: 1440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL L 477 " -0.007 2.00e-02 2.50e+03 1.37e-02 1.87e+00 pdb=" C VAL L 477 " 0.024 2.00e-02 2.50e+03 pdb=" O VAL L 477 " -0.009 2.00e-02 2.50e+03 pdb=" N SER L 478 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 477 " 0.007 2.00e-02 2.50e+03 1.35e-02 1.81e+00 pdb=" C VAL F 477 " -0.023 2.00e-02 2.50e+03 pdb=" O VAL F 477 " 0.009 2.00e-02 2.50e+03 pdb=" N SER F 478 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL J 477 " -0.007 2.00e-02 2.50e+03 1.34e-02 1.81e+00 pdb=" C VAL J 477 " 0.023 2.00e-02 2.50e+03 pdb=" O VAL J 477 " -0.009 2.00e-02 2.50e+03 pdb=" N SER J 478 " -0.008 2.00e-02 2.50e+03 ... (remaining 1437 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 3005 2.89 - 3.40: 9513 3.40 - 3.90: 13326 3.90 - 4.40: 16411 4.40 - 4.90: 24944 Nonbonded interactions: 67199 Sorted by model distance: nonbonded pdb=" NE2 GLN J 441 " pdb=" OD1 ASP J 495 " model vdw 2.393 2.520 nonbonded pdb=" NE2 GLN C 441 " pdb=" OD1 ASP C 495 " model vdw 2.393 2.520 nonbonded pdb=" NE2 GLN E 441 " pdb=" OD1 ASP E 495 " model vdw 2.393 2.520 nonbonded pdb=" NE2 GLN F 441 " pdb=" OD1 ASP F 495 " model vdw 2.393 2.520 nonbonded pdb=" NE2 GLN I 441 " pdb=" OD1 ASP I 495 " model vdw 2.393 2.520 ... (remaining 67194 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' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 5100 2.51 5 N 1452 2.21 5 O 1680 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.330 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: 2.440 Check model and map are aligned: 0.120 Convert atoms to be neutral: 0.060 Process input model: 24.660 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5556 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.034 8328 Z= 0.446 Angle : 1.001 5.193 11184 Z= 0.590 Chirality : 0.051 0.199 1332 Planarity : 0.005 0.022 1440 Dihedral : 10.654 67.080 3276 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.39 (0.21), residues: 1020 helix: -2.55 (0.13), residues: 780 sheet: None (None), residues: 0 loop : -0.14 (0.43), residues: 240 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 417 time to evaluate : 1.177 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 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: 0 outliers final: 0 residues processed: 417 average time/residue: 0.2920 time to fit residues: 149.7290 Evaluate side-chains 215 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 1.084 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 24 optimal weight: 20.0000 chunk 49 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 56 optimal weight: 20.0000 chunk 87 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 GLN A 512 ASN B 497 GLN C 437 GLN ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 497 GLN D 512 ASN E 497 GLN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 514 GLN I 458 GLN K 514 GLN ** L 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6069 moved from start: 0.7044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 8328 Z= 0.240 Angle : 0.722 8.487 11184 Z= 0.383 Chirality : 0.043 0.230 1332 Planarity : 0.006 0.095 1440 Dihedral : 5.588 20.926 1092 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.21), residues: 1020 helix: -1.02 (0.14), residues: 840 sheet: None (None), residues: 0 loop : -0.86 (0.38), residues: 180 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 328 time to evaluate : 1.325 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 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: 0 outliers final: 0 residues processed: 328 average time/residue: 0.2536 time to fit residues: 105.7852 Evaluate side-chains 211 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 1.086 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 30.0000 chunk 27 optimal weight: 0.9990 chunk 72 optimal weight: 20.0000 chunk 59 optimal weight: 0.9980 chunk 24 optimal weight: 30.0000 chunk 87 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 86 optimal weight: 0.2980 chunk 29 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 GLN ** C 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 GLN E 497 GLN E 512 ASN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN F 449 ASN ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 512 ASN G 514 GLN H 457 ASN H 497 GLN H 507 GLN ** H 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 497 GLN K 512 ASN L 450 GLN ** L 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 1.0236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.080 8328 Z= 0.238 Angle : 0.713 13.327 11184 Z= 0.381 Chirality : 0.042 0.201 1332 Planarity : 0.004 0.044 1440 Dihedral : 5.420 23.562 1092 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.23), residues: 1020 helix: -0.57 (0.15), residues: 888 sheet: None (None), residues: 0 loop : -1.37 (0.48), residues: 132 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 350 time to evaluate : 1.102 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 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: 2 outliers final: 0 residues processed: 351 average time/residue: 0.2418 time to fit residues: 109.4429 Evaluate side-chains 237 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 1.048 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 ASN C 458 GLN ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 512 ASN ** H 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 512 ASN K 512 ASN L 441 GLN L 458 GLN L 497 GLN ** L 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 moved from start: 1.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.076 8328 Z= 0.206 Angle : 0.654 6.606 11184 Z= 0.350 Chirality : 0.041 0.174 1332 Planarity : 0.005 0.063 1440 Dihedral : 5.256 22.006 1092 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 20.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.61 (0.24), residues: 1020 helix: -0.08 (0.16), residues: 888 sheet: None (None), residues: 0 loop : -1.71 (0.46), residues: 132 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 342 time to evaluate : 1.137 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.2363 time to fit residues: 105.0226 Evaluate side-chains 246 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 1.103 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 64 optimal weight: 20.0000 chunk 0 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 83 optimal weight: 9.9990 chunk 23 optimal weight: 0.0040 chunk 31 optimal weight: 0.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 ASN ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 ASN ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 437 GLN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 512 ASN ** G 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 512 ASN ** H 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 450 GLN I 489 GLN I 512 ASN ** J 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 512 ASN L 512 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 1.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 8328 Z= 0.210 Angle : 0.661 6.801 11184 Z= 0.351 Chirality : 0.041 0.176 1332 Planarity : 0.005 0.085 1440 Dihedral : 5.113 22.219 1092 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.21 (0.25), residues: 1020 helix: 0.22 (0.17), residues: 888 sheet: None (None), residues: 0 loop : -1.85 (0.45), residues: 132 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 348 time to evaluate : 1.090 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 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: 0 outliers final: 0 residues processed: 348 average time/residue: 0.2262 time to fit residues: 102.4545 Evaluate side-chains 252 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 1.106 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 22 optimal weight: 0.2980 chunk 92 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 43 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 30.0000 chunk 89 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 ASN ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 ASN F 437 GLN ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 512 ASN G 512 ASN ** H 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 512 ASN ** J 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 512 ASN L 512 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 1.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 8328 Z= 0.233 Angle : 0.693 7.648 11184 Z= 0.369 Chirality : 0.042 0.240 1332 Planarity : 0.005 0.065 1440 Dihedral : 5.098 20.842 1092 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 21.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.25), residues: 1020 helix: 0.07 (0.16), residues: 888 sheet: None (None), residues: 0 loop : -1.83 (0.46), residues: 132 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 384 time to evaluate : 1.101 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 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: 0 outliers final: 0 residues processed: 384 average time/residue: 0.2342 time to fit residues: 116.9347 Evaluate side-chains 286 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 1.082 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 92 optimal weight: 0.2980 chunk 57 optimal weight: 0.9990 chunk 56 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 GLN B 512 ASN C 449 ASN ** D 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 457 ASN ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 512 ASN ** H 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 512 ASN ** J 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 450 GLN K 512 ASN K 514 GLN L 512 ASN L 514 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 1.5218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 8328 Z= 0.214 Angle : 0.696 8.446 11184 Z= 0.364 Chirality : 0.043 0.194 1332 Planarity : 0.004 0.055 1440 Dihedral : 5.168 20.989 1092 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 20.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.39 (0.25), residues: 1020 helix: 0.07 (0.17), residues: 888 sheet: None (None), residues: 0 loop : -1.68 (0.47), residues: 132 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 395 time to evaluate : 1.121 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 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: 2 outliers final: 0 residues processed: 396 average time/residue: 0.2151 time to fit residues: 112.7814 Evaluate side-chains 301 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 301 time to evaluate : 1.101 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 8 optimal weight: 20.0000 chunk 72 optimal weight: 20.0000 chunk 84 optimal weight: 8.9990 chunk 88 optimal weight: 20.0000 chunk 80 optimal weight: 20.0000 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 GLN B 512 ASN ** C 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 GLN ** D 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN ** F 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 512 ASN ** H 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 514 GLN ** I 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 512 ASN L 512 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 1.5843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 8328 Z= 0.200 Angle : 0.680 8.168 11184 Z= 0.358 Chirality : 0.042 0.151 1332 Planarity : 0.004 0.058 1440 Dihedral : 5.148 24.326 1092 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 19.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.12 (0.25), residues: 1020 helix: 0.27 (0.17), residues: 888 sheet: None (None), residues: 0 loop : -1.72 (0.49), residues: 132 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 392 time to evaluate : 1.100 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 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: 1 outliers final: 0 residues processed: 392 average time/residue: 0.2192 time to fit residues: 112.8861 Evaluate side-chains 310 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 310 time to evaluate : 1.021 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.0770 chunk 88 optimal weight: 20.0000 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 67 optimal weight: 0.5980 chunk 26 optimal weight: 8.9990 chunk 77 optimal weight: 6.9990 chunk 81 optimal weight: 8.9990 chunk 85 optimal weight: 8.9990 chunk 56 optimal weight: 30.0000 chunk 91 optimal weight: 4.9990 overall best weight: 2.9344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 ASN C 449 ASN D 441 GLN ** D 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 512 ASN G 512 ASN ** H 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 497 GLN ** J 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 512 ASN K 514 GLN ** L 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 1.7632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 8328 Z= 0.283 Angle : 0.794 8.164 11184 Z= 0.419 Chirality : 0.045 0.185 1332 Planarity : 0.005 0.055 1440 Dihedral : 5.657 26.970 1092 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 23.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.38 (0.25), residues: 1020 helix: 0.05 (0.17), residues: 888 sheet: None (None), residues: 0 loop : -1.47 (0.52), residues: 132 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 432 time to evaluate : 1.075 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 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: 0 outliers final: 0 residues processed: 432 average time/residue: 0.2099 time to fit residues: 120.3060 Evaluate side-chains 336 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 336 time to evaluate : 1.026 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 88 optimal weight: 20.0000 chunk 76 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 ASN C 450 GLN ** D 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 507 GLN ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 512 ASN ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 512 ASN G 514 GLN ** H 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 450 GLN ** I 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 512 ASN L 512 ASN L 514 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 1.8229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 8328 Z= 0.260 Angle : 0.798 8.364 11184 Z= 0.418 Chirality : 0.045 0.182 1332 Planarity : 0.004 0.063 1440 Dihedral : 5.607 24.226 1092 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 23.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.25), residues: 1020 helix: -0.00 (0.17), residues: 888 sheet: None (None), residues: 0 loop : -1.64 (0.52), residues: 132 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 427 time to evaluate : 1.181 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 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: 0 outliers final: 0 residues processed: 427 average time/residue: 0.2275 time to fit residues: 127.7800 Evaluate side-chains 346 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 346 time to evaluate : 1.079 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 chunk 11 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 GLN C 497 GLN ** D 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 450 GLN ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 512 ASN ** G 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 450 GLN ** I 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 512 ASN K 514 GLN L 512 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.068971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.055258 restraints weight = 36828.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.057289 restraints weight = 24709.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.058791 restraints weight = 18260.826| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 1.8607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 8328 Z= 0.237 Angle : 0.795 11.924 11184 Z= 0.418 Chirality : 0.045 0.179 1332 Planarity : 0.004 0.061 1440 Dihedral : 5.471 22.944 1092 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 21.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.52 (0.25), residues: 1020 helix: -0.00 (0.17), residues: 888 sheet: None (None), residues: 0 loop : -1.83 (0.52), residues: 132 =============================================================================== Job complete usr+sys time: 2268.43 seconds wall clock time: 41 minutes 54.26 seconds (2514.26 seconds total)