Starting phenix.real_space_refine (version: dev) on Sun Feb 19 17:47:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7myn_24081/02_2023/7myn_24081.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7myn_24081/02_2023/7myn_24081.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7myn_24081/02_2023/7myn_24081.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7myn_24081/02_2023/7myn_24081.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7myn_24081/02_2023/7myn_24081.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7myn_24081/02_2023/7myn_24081.pdb" } resolution = 2.79 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= 0.394 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 Process input model Symmetric amino acids flipped Residue "A GLU 52": "OE1" <-> "OE2" Residue "A GLU 80": "OE1" <-> "OE2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "A TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 263": "OE1" <-> "OE2" Residue "A TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 488": "OD1" <-> "OD2" Residue "A GLU 545": "OE1" <-> "OE2" Residue "A ASP 549": "OD1" <-> "OD2" Residue "A GLU 707": "OE1" <-> "OE2" Residue "A ASP 830": "OD1" <-> "OD2" Residue "A TYR 836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 926": "OD1" <-> "OD2" Residue "A TYR 988": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 411": "OE1" <-> "OE2" Residue "B TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 468": "OE1" <-> "OE2" Residue "B GLU 485": "OE1" <-> "OE2" Residue "B GLU 495": "OE1" <-> "OE2" Residue "B GLU 555": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 10426 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8072 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 977, 7981 Classifications: {'peptide': 977} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 929} Chain breaks: 5 Conformer: "B" Number of residues, atoms: 977, 7981 Classifications: {'peptide': 977} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 929} Chain breaks: 5 bond proxies already assigned to first conformer: 8063 Chain: "B" Number of atoms: 2346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2346 Classifications: {'peptide': 276} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 271} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Residues with excluded nonbonded symmetry interactions: 11 residue: pdb=" N AILE A 932 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE A 932 " occ=0.50 residue: pdb=" N AASP A 933 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP A 933 " occ=0.50 residue: pdb=" N APHE A 934 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 934 " occ=0.50 residue: pdb=" N AGLY A 935 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 935 " occ=0.50 residue: pdb=" N AGLU A 950 " occ=0.54 ... (16 atoms not shown) pdb=" OE2BGLU A 950 " occ=0.46 residue: pdb=" N AARG A 951 " occ=0.54 ... (20 atoms not shown) pdb=" NH2BARG A 951 " occ=0.46 residue: pdb=" N AVAL A 952 " occ=0.54 ... (12 atoms not shown) pdb=" CG2BVAL A 952 " occ=0.46 residue: pdb=" N APRO A 953 " occ=0.54 ... (12 atoms not shown) pdb=" CD BPRO A 953 " occ=0.46 residue: pdb=" N APHE A 954 " occ=0.54 ... (20 atoms not shown) pdb=" CZ BPHE A 954 " occ=0.46 residue: pdb=" N AVAL A 955 " occ=0.54 ... (12 atoms not shown) pdb=" CG2BVAL A 955 " occ=0.46 residue: pdb=" N ALEU A 956 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU A 956 " occ=0.50 Time building chain proxies: 10.86, per 1000 atoms: 1.04 Number of scatterers: 10426 At special positions: 0 Unit cell: (86.735, 129.58, 110.77, 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 73 16.00 O 1920 8.00 N 1800 7.00 C 6633 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: 4.00 Conformation dependent library (CDL) restraints added in 2.7 seconds 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2418 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 10 sheets defined 52.5% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 41 through 52 removed outlier: 3.765A pdb=" N GLU A 52 " --> pdb=" O GLU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 68 Processing helix chain 'A' and resid 89 through 93 removed outlier: 4.021A pdb=" N ARG A 93 " --> pdb=" O CYS A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 122 Processing helix chain 'A' and resid 125 through 131 Processing helix chain 'A' and resid 133 through 155 removed outlier: 4.113A pdb=" N LEU A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ASN A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL A 146 " --> pdb=" O ASN A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 167 Processing helix chain 'A' and resid 178 through 183 Processing helix chain 'A' and resid 216 through 229 Processing helix chain 'A' and resid 266 through 269 Processing helix chain 'A' and resid 270 through 280 Processing helix chain 'A' and resid 290 through 297 Processing helix chain 'A' and resid 305 through 309 removed outlier: 3.634A pdb=" N SER A 308 " --> pdb=" O PRO A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 496 Processing helix chain 'A' and resid 528 through 537 removed outlier: 3.666A pdb=" N LYS A 532 " --> pdb=" O LYS A 528 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG A 537 " --> pdb=" O ALA A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 554 Processing helix chain 'A' and resid 556 through 563 removed outlier: 3.886A pdb=" N VAL A 559 " --> pdb=" O HIS A 556 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR A 560 " --> pdb=" O TYR A 557 " (cutoff:3.500A) Proline residue: A 562 - end of helix Processing helix chain 'A' and resid 564 through 572 Processing helix chain 'A' and resid 576 through 589 removed outlier: 3.634A pdb=" N ASP A 589 " --> pdb=" O CYS A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 599 Processing helix chain 'A' and resid 600 through 603 Processing helix chain 'A' and resid 608 through 622 Processing helix chain 'A' and resid 624 through 631 Processing helix chain 'A' and resid 631 through 638 Processing helix chain 'A' and resid 647 through 658 removed outlier: 3.575A pdb=" N ARG A 651 " --> pdb=" O ASN A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 673 removed outlier: 3.773A pdb=" N PHE A 666 " --> pdb=" O ARG A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 695 Processing helix chain 'A' and resid 697 through 721 removed outlier: 3.884A pdb=" N HIS A 701 " --> pdb=" O MET A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 741 removed outlier: 3.844A pdb=" N ARG A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 749 Processing helix chain 'A' and resid 807 through 828 Processing helix chain 'A' and resid 857 through 865 Processing helix chain 'A' and resid 875 through 885 removed outlier: 3.573A pdb=" N ASN A 885 " --> pdb=" O LEU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 888 No H-bonds generated for 'chain 'A' and resid 886 through 888' Processing helix chain 'A' and resid 889 through 912 Processing helix chain 'A' and resid 957 through 965 removed outlier: 4.018A pdb=" N VAL A 963 " --> pdb=" O ASP A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 994 Processing helix chain 'A' and resid 994 through 1004 removed outlier: 3.729A pdb=" N PHE A 998 " --> pdb=" O HIS A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1009 removed outlier: 3.554A pdb=" N SER A1008 " --> pdb=" O MET A1005 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY A1009 " --> pdb=" O LEU A1006 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1005 through 1009' Processing helix chain 'A' and resid 1015 through 1026 removed outlier: 3.932A pdb=" N ILE A1019 " --> pdb=" O SER A1015 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TYR A1021 " --> pdb=" O ASP A1017 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE A1022 " --> pdb=" O ASP A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1048 removed outlier: 4.087A pdb=" N LEU A1036 " --> pdb=" O GLU A1032 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU A1037 " --> pdb=" O GLN A1033 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 331 Processing helix chain 'B' and resid 339 through 347 removed outlier: 3.622A pdb=" N VAL B 343 " --> pdb=" O SER B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 removed outlier: 4.161A pdb=" N GLY B 388 " --> pdb=" O HIS B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 411 Processing helix chain 'B' and resid 412 through 416 removed outlier: 3.922A pdb=" N GLN B 415 " --> pdb=" O SER B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 436 removed outlier: 3.745A pdb=" N GLN B 435 " --> pdb=" O GLN B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 507 removed outlier: 4.691A pdb=" N GLU B 507 " --> pdb=" O ARG B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 516 removed outlier: 3.656A pdb=" N PHE B 512 " --> pdb=" O TYR B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 587 removed outlier: 3.880A pdb=" N ILE B 521 " --> pdb=" O ASN B 517 " (cutoff:3.500A) Proline residue: B 568 - end of helix Processing helix chain 'B' and resid 590 through 596 removed outlier: 3.695A pdb=" N LEU B 594 " --> pdb=" O ARG B 590 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU B 596 " --> pdb=" O LYS B 592 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 22 removed outlier: 3.844A pdb=" N ILE A 20 " --> pdb=" O CYS A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 82 removed outlier: 4.154A pdb=" N PHE A 70 " --> pdb=" O PHE A 82 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 205 through 211 Processing sheet with id=AA4, first strand: chain 'A' and resid 260 through 261 removed outlier: 4.201A pdb=" N LEU A 252 " --> pdb=" O PHE A 261 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 382 through 392 removed outlier: 6.382A pdb=" N TRP A 383 " --> pdb=" O CYS A 340 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N CYS A 340 " --> pdb=" O TRP A 383 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LEU A 334 " --> pdb=" O TYR A 389 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLU A 474 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ALA A 341 " --> pdb=" O CYS A 472 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N CYS A 472 " --> pdb=" O ALA A 341 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 365 through 366 removed outlier: 3.870A pdb=" N GLU A 365 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LYS A 353 " --> pdb=" O VAL A 409 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 371 through 372 removed outlier: 5.085A pdb=" N LYS A 353 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N SER A 408 " --> pdb=" O PRO A 421 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N LYS A 410 " --> pdb=" O HIS A 419 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N HIS A 419 " --> pdb=" O LYS A 410 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 779 through 783 removed outlier: 6.706A pdb=" N VAL A 845 " --> pdb=" O ILE A 841 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 854 through 856 Processing sheet with id=AB1, first strand: chain 'B' and resid 334 through 336 515 hydrogen bonds defined for protein. 1467 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: 3.39 Time building geometry restraints manager: 4.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3427 1.35 - 1.46: 2328 1.46 - 1.58: 4770 1.58 - 1.70: 0 1.70 - 1.82: 114 Bond restraints: 10639 Sorted by residual: bond pdb=" CB ASN A 157 " pdb=" CG ASN A 157 " ideal model delta sigma weight residual 1.516 1.548 -0.032 2.50e-02 1.60e+03 1.65e+00 bond pdb=" CA LYS A 264 " pdb=" CB LYS A 264 " ideal model delta sigma weight residual 1.526 1.541 -0.016 1.25e-02 6.40e+03 1.55e+00 bond pdb=" CB ASN A 803 " pdb=" CG ASN A 803 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.51e+00 bond pdb=" CD GLU B 458 " pdb=" OE1 GLU B 458 " ideal model delta sigma weight residual 1.249 1.226 0.023 1.90e-02 2.77e+03 1.43e+00 bond pdb=" CA ASN A 157 " pdb=" CB ASN A 157 " ideal model delta sigma weight residual 1.526 1.544 -0.019 1.68e-02 3.54e+03 1.24e+00 ... (remaining 10634 not shown) Histogram of bond angle deviations from ideal: 98.75 - 105.80: 216 105.80 - 112.85: 5549 112.85 - 119.91: 3702 119.91 - 126.96: 4749 126.96 - 134.01: 136 Bond angle restraints: 14352 Sorted by residual: angle pdb=" N VAL A 105 " pdb=" CA VAL A 105 " pdb=" C VAL A 105 " ideal model delta sigma weight residual 113.20 108.84 4.36 9.60e-01 1.09e+00 2.06e+01 angle pdb=" C ILE A 102 " pdb=" N GLU A 103 " pdb=" CA GLU A 103 " ideal model delta sigma weight residual 121.03 128.10 -7.07 1.60e+00 3.91e-01 1.96e+01 angle pdb=" N GLU B 458 " pdb=" CA GLU B 458 " pdb=" CB GLU B 458 " ideal model delta sigma weight residual 110.16 116.28 -6.12 1.48e+00 4.57e-01 1.71e+01 angle pdb=" N ASN A 157 " pdb=" CA ASN A 157 " pdb=" C ASN A 157 " ideal model delta sigma weight residual 110.44 106.22 4.22 1.20e+00 6.94e-01 1.24e+01 angle pdb=" CA TYR A 265 " pdb=" CB TYR A 265 " pdb=" CG TYR A 265 " ideal model delta sigma weight residual 113.90 119.87 -5.97 1.80e+00 3.09e-01 1.10e+01 ... (remaining 14347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 5830 17.97 - 35.93: 573 35.93 - 53.90: 78 53.90 - 71.86: 18 71.86 - 89.83: 9 Dihedral angle restraints: 6508 sinusoidal: 2781 harmonic: 3727 Sorted by residual: dihedral pdb=" CA GLU A 81 " pdb=" C GLU A 81 " pdb=" N PHE A 82 " pdb=" CA PHE A 82 " ideal model delta harmonic sigma weight residual -180.00 -156.29 -23.71 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA GLU A 48 " pdb=" C GLU A 48 " pdb=" N LEU A 49 " pdb=" CA LEU A 49 " ideal model delta harmonic sigma weight residual 180.00 157.28 22.72 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA SER A 405 " pdb=" C SER A 405 " pdb=" N ILE A 406 " pdb=" CA ILE A 406 " ideal model delta harmonic sigma weight residual 180.00 161.91 18.09 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 6505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1084 0.041 - 0.082: 347 0.082 - 0.124: 93 0.124 - 0.165: 24 0.165 - 0.206: 3 Chirality restraints: 1551 Sorted by residual: chirality pdb=" CA GLU A 223 " pdb=" N GLU A 223 " pdb=" C GLU A 223 " pdb=" CB GLU A 223 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA GLU A 48 " pdb=" N GLU A 48 " pdb=" C GLU A 48 " pdb=" CB GLU A 48 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.71e-01 chirality pdb=" CA ILE A 338 " pdb=" N ILE A 338 " pdb=" C ILE A 338 " pdb=" CB ILE A 338 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.07e-01 ... (remaining 1548 not shown) Planarity restraints: 1848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 708 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.62e+00 pdb=" C ALA A 708 " -0.044 2.00e-02 2.50e+03 pdb=" O ALA A 708 " 0.017 2.00e-02 2.50e+03 pdb=" N MET A 709 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 195 " 0.017 2.00e-02 2.50e+03 1.60e-02 6.42e+00 pdb=" CG TRP A 195 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP A 195 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP A 195 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 195 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 195 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 195 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 195 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 195 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 195 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 707 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.66e+00 pdb=" C GLU A 707 " -0.041 2.00e-02 2.50e+03 pdb=" O GLU A 707 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA A 708 " 0.014 2.00e-02 2.50e+03 ... (remaining 1845 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2664 2.80 - 3.33: 10112 3.33 - 3.85: 17934 3.85 - 4.38: 20765 4.38 - 4.90: 35084 Nonbonded interactions: 86559 Sorted by model distance: nonbonded pdb=" O PHE A 430 " pdb=" OH TYR A 644 " model vdw 2.280 2.440 nonbonded pdb=" OH TYR A 584 " pdb=" OD1 ASP A 608 " model vdw 2.290 2.440 nonbonded pdb=" OG1 THR A 41 " pdb=" O GLU A 85 " model vdw 2.293 2.440 nonbonded pdb=" O BARG A 951 " pdb=" OH TYR A1021 " model vdw 2.300 2.440 nonbonded pdb=" OD1 ASP A 454 " pdb=" NH1 ARG B 348 " model vdw 2.303 2.520 ... (remaining 86554 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 73 5.16 5 C 6633 2.51 5 N 1800 2.21 5 O 1920 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=0.46 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.070 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: 1.640 Check model and map are aligned: 0.140 Process input model: 36.670 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.090 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:13.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 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 : 0.003 0.035 10639 Z= 0.191 Angle : 0.712 10.836 14352 Z= 0.372 Chirality : 0.045 0.206 1551 Planarity : 0.005 0.044 1848 Dihedral : 14.110 89.827 4090 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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 (0.22), residues: 1252 helix: 0.43 (0.20), residues: 577 sheet: -1.13 (0.42), residues: 138 loop : -0.68 (0.26), residues: 537 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 331 time to evaluate : 1.348 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 331 average time/residue: 1.2243 time to fit residues: 436.2334 Evaluate side-chains 242 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 1.249 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 8.9990 chunk 93 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 97 optimal weight: 20.0000 chunk 37 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 112 optimal weight: 10.0000 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 157 ASN ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 630 GLN ** A 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 GLN ** A1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 10639 Z= 0.265 Angle : 0.655 9.798 14352 Z= 0.328 Chirality : 0.043 0.149 1551 Planarity : 0.004 0.058 1848 Dihedral : 4.454 26.835 1385 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer Outliers : 2.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.18 (0.23), residues: 1252 helix: 1.03 (0.21), residues: 595 sheet: -1.09 (0.39), residues: 161 loop : -0.45 (0.28), residues: 496 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 251 time to evaluate : 1.315 Fit side-chains outliers start: 28 outliers final: 9 residues processed: 263 average time/residue: 1.2163 time to fit residues: 345.2824 Evaluate side-chains 236 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 227 time to evaluate : 1.216 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 3 residues processed: 6 average time/residue: 0.5844 time to fit residues: 5.7322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 5.9990 chunk 34 optimal weight: 0.0270 chunk 93 optimal weight: 9.9990 chunk 76 optimal weight: 7.9990 chunk 31 optimal weight: 0.9980 chunk 112 optimal weight: 20.0000 chunk 121 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 overall best weight: 3.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 HIS A 728 GLN ** A 917 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 GLN ** A1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 488 ASN ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 10639 Z= 0.268 Angle : 0.631 9.661 14352 Z= 0.316 Chirality : 0.042 0.146 1551 Planarity : 0.004 0.042 1848 Dihedral : 4.402 27.020 1385 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer Outliers : 3.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.36 (0.24), residues: 1252 helix: 1.25 (0.21), residues: 596 sheet: -1.04 (0.41), residues: 145 loop : -0.49 (0.28), residues: 511 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 235 time to evaluate : 1.136 Fit side-chains outliers start: 37 outliers final: 16 residues processed: 250 average time/residue: 1.2106 time to fit residues: 327.6571 Evaluate side-chains 235 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 219 time to evaluate : 1.406 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 7 residues processed: 9 average time/residue: 0.6283 time to fit residues: 8.0834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 chunk 119 optimal weight: 20.0000 chunk 59 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 HIS A 630 GLN A 958 GLN ** A1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 10639 Z= 0.214 Angle : 0.612 9.943 14352 Z= 0.306 Chirality : 0.042 0.237 1551 Planarity : 0.004 0.042 1848 Dihedral : 4.296 26.333 1385 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer Outliers : 2.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.47 (0.24), residues: 1252 helix: 1.40 (0.21), residues: 596 sheet: -1.05 (0.41), residues: 145 loop : -0.50 (0.28), residues: 511 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 234 time to evaluate : 1.222 Fit side-chains outliers start: 31 outliers final: 16 residues processed: 248 average time/residue: 1.1578 time to fit residues: 311.2739 Evaluate side-chains 237 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 221 time to evaluate : 1.205 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 9 residues processed: 7 average time/residue: 0.7895 time to fit residues: 8.0798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 5.9990 chunk 68 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 102 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 chunk 0 optimal weight: 50.0000 chunk 61 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN A 157 ASN ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 HIS A 370 ASN ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 728 GLN A 958 GLN B 385 HIS ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.060 10639 Z= 0.461 Angle : 0.706 9.562 14352 Z= 0.353 Chirality : 0.046 0.164 1551 Planarity : 0.004 0.042 1848 Dihedral : 4.589 29.593 1385 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer Outliers : 3.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.23 (0.24), residues: 1252 helix: 1.21 (0.21), residues: 599 sheet: -1.33 (0.40), residues: 144 loop : -0.57 (0.28), residues: 509 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 229 time to evaluate : 1.431 Fit side-chains revert: symmetry clash outliers start: 43 outliers final: 17 residues processed: 252 average time/residue: 1.1897 time to fit residues: 325.0357 Evaluate side-chains 233 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 216 time to evaluate : 1.148 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 8 residues processed: 9 average time/residue: 0.4581 time to fit residues: 6.4476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 119 optimal weight: 20.0000 chunk 99 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 62 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: A 59 HIS A 75 GLN ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN A 444 ASN A 450 HIS A 630 GLN A 647 ASN A 728 GLN ** A 917 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 GLN ** A1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 385 HIS ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 10639 Z= 0.182 Angle : 0.638 11.102 14352 Z= 0.314 Chirality : 0.042 0.179 1551 Planarity : 0.004 0.037 1848 Dihedral : 4.365 31.084 1385 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer Outliers : 2.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 (0.24), residues: 1252 helix: 1.40 (0.21), residues: 598 sheet: -1.11 (0.41), residues: 145 loop : -0.44 (0.28), residues: 509 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 233 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 13 residues processed: 250 average time/residue: 1.0768 time to fit residues: 294.0271 Evaluate side-chains 235 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 222 time to evaluate : 1.243 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 9 residues processed: 4 average time/residue: 0.9744 time to fit residues: 6.0154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 40.0000 chunk 13 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 87 optimal weight: 0.0770 chunk 67 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 119 optimal weight: 20.0000 chunk 74 optimal weight: 8.9990 chunk 72 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 overall best weight: 2.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 HIS A 630 GLN A 738 GLN ** A 917 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 10639 Z= 0.231 Angle : 0.663 10.654 14352 Z= 0.329 Chirality : 0.043 0.168 1551 Planarity : 0.004 0.041 1848 Dihedral : 4.355 33.547 1385 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer Outliers : 2.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.46 (0.24), residues: 1252 helix: 1.41 (0.21), residues: 596 sheet: -1.20 (0.41), residues: 151 loop : -0.46 (0.28), residues: 505 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 240 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 11 residues processed: 253 average time/residue: 1.1407 time to fit residues: 313.5863 Evaluate side-chains 241 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 230 time to evaluate : 1.261 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 3 average time/residue: 0.6741 time to fit residues: 4.0393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 11 optimal weight: 0.0770 chunk 93 optimal weight: 4.9990 chunk 108 optimal weight: 40.0000 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS A 60 GLN A 75 GLN A 157 ASN ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 HIS A 630 GLN ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 917 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 10639 Z= 0.291 Angle : 0.702 10.834 14352 Z= 0.347 Chirality : 0.044 0.188 1551 Planarity : 0.004 0.035 1848 Dihedral : 4.495 33.814 1385 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 2.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.46 (0.24), residues: 1252 helix: 1.40 (0.21), residues: 595 sheet: -1.20 (0.41), residues: 149 loop : -0.45 (0.28), residues: 508 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 233 time to evaluate : 1.318 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 11 residues processed: 248 average time/residue: 1.1852 time to fit residues: 320.4650 Evaluate side-chains 230 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 219 time to evaluate : 1.276 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 7 residues processed: 4 average time/residue: 0.6120 time to fit residues: 4.8082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 chunk 111 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 34 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 73 optimal weight: 20.0000 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN A 450 HIS A 630 GLN ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 917 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 ASN ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 10639 Z= 0.332 Angle : 0.731 12.210 14352 Z= 0.362 Chirality : 0.045 0.184 1551 Planarity : 0.004 0.045 1848 Dihedral : 4.583 33.368 1385 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.34 (0.24), residues: 1252 helix: 1.32 (0.21), residues: 596 sheet: -1.25 (0.41), residues: 147 loop : -0.54 (0.27), residues: 509 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 221 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 11 residues processed: 231 average time/residue: 1.1433 time to fit residues: 288.1038 Evaluate side-chains 226 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 215 time to evaluate : 1.237 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 4 average time/residue: 0.9337 time to fit residues: 5.9459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 chunk 55 optimal weight: 0.9980 chunk 81 optimal weight: 10.0000 chunk 123 optimal weight: 20.0000 chunk 113 optimal weight: 20.0000 chunk 98 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 630 GLN A 738 GLN ** A 917 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.050 10639 Z= 0.362 Angle : 0.745 11.162 14352 Z= 0.373 Chirality : 0.046 0.228 1551 Planarity : 0.004 0.032 1848 Dihedral : 4.660 32.622 1385 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer Outliers : 1.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.27 (0.23), residues: 1252 helix: 1.29 (0.21), residues: 588 sheet: -1.34 (0.40), residues: 147 loop : -0.56 (0.27), residues: 517 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 223 time to evaluate : 1.193 Fit side-chains outliers start: 14 outliers final: 9 residues processed: 232 average time/residue: 1.0766 time to fit residues: 271.7167 Evaluate side-chains 225 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 216 time to evaluate : 1.098 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 2 average time/residue: 0.1590 time to fit residues: 2.0266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 98 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 101 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 630 GLN A 738 GLN ** A 917 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.167212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.110060 restraints weight = 21837.568| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 3.48 r_work: 0.3095 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4000 r_free = 0.4000 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4000 r_free = 0.4000 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 10639 Z= 0.324 Angle : 0.753 11.593 14352 Z= 0.373 Chirality : 0.045 0.214 1551 Planarity : 0.004 0.033 1848 Dihedral : 4.693 32.883 1385 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.23 (0.23), residues: 1252 helix: 1.26 (0.21), residues: 588 sheet: -1.37 (0.39), residues: 147 loop : -0.59 (0.27), residues: 517 =============================================================================== Job complete usr+sys time: 4868.67 seconds wall clock time: 87 minutes 20.43 seconds (5240.43 seconds total)