Starting phenix.real_space_refine on Wed Feb 14 22:30:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7myn_24081/02_2024/7myn_24081.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7myn_24081/02_2024/7myn_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_2024/7myn_24081.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7myn_24081/02_2024/7myn_24081.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7myn_24081/02_2024/7myn_24081.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7myn_24081/02_2024/7myn_24081.pdb" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 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. 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-5238/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: 9.33, per 1000 atoms: 0.89 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: 4.10 Conformation dependent library (CDL) restraints added in 3.4 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: 1.20 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: 3.73 Time building geometry restraints manager: 4.45 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 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: 0.950 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 36.540 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 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 % Allowed : 0.43 % Favored : 99.31 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 195 HIS 0.003 0.001 HIS A 180 PHE 0.017 0.002 PHE A 734 TYR 0.024 0.001 TYR A 207 ARG 0.009 0.000 ARG A 382 *********************** 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 : 1.194 Fit side-chains revert: symmetry clash REVERT: A 59 HIS cc_start: 0.8156 (p90) cc_final: 0.7913 (p90) REVERT: A 81 GLU cc_start: 0.7894 (pp20) cc_final: 0.7307 (pp20) REVERT: A 83 PHE cc_start: 0.7518 (m-80) cc_final: 0.6542 (m-80) REVERT: A 85 GLU cc_start: 0.7884 (mp0) cc_final: 0.7414 (mp0) REVERT: A 179 LYS cc_start: 0.8412 (mppt) cc_final: 0.8139 (mppt) REVERT: A 191 ILE cc_start: 0.8659 (mm) cc_final: 0.8293 (mp) REVERT: A 195 TRP cc_start: 0.8108 (m100) cc_final: 0.7615 (m100) REVERT: A 205 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.7369 (pp30) REVERT: A 219 GLN cc_start: 0.8296 (pt0) cc_final: 0.8075 (pt0) REVERT: A 264 LYS cc_start: 0.8014 (ptmm) cc_final: 0.7721 (pptt) REVERT: A 710 GLU cc_start: 0.7644 (pp20) cc_final: 0.7314 (pp20) REVERT: A 882 LYS cc_start: 0.8288 (mmmt) cc_final: 0.7998 (mmmt) REVERT: A 976 GLU cc_start: 0.7297 (mp0) cc_final: 0.6930 (mm-30) REVERT: A 1010 MET cc_start: 0.7458 (mpp) cc_final: 0.6927 (mpt) REVERT: B 326 MET cc_start: 0.6988 (tpp) cc_final: 0.6073 (tpp) REVERT: B 485 GLU cc_start: 0.8044 (tp30) cc_final: 0.7680 (tp30) REVERT: B 496 GLU cc_start: 0.8508 (tp30) cc_final: 0.7864 (tp30) REVERT: B 499 GLN cc_start: 0.7424 (tm-30) cc_final: 0.6974 (tm-30) REVERT: B 525 MET cc_start: 0.7838 (mmp) cc_final: 0.7349 (mmp) REVERT: B 535 ILE cc_start: 0.8755 (pt) cc_final: 0.8464 (pp) outliers start: 1 outliers final: 0 residues processed: 331 average time/residue: 1.2268 time to fit residues: 436.6622 Evaluate side-chains 246 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 245 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 GLN 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: 5.9990 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 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 HIS A 630 GLN ** A 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 ASN ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1770 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= 0.259 Angle : 0.628 10.143 14352 Z= 0.315 Chirality : 0.042 0.148 1551 Planarity : 0.004 0.043 1848 Dihedral : 4.567 45.480 1388 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.76 % Allowed : 14.47 % Favored : 82.77 % 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: 0.17 (0.23), residues: 1252 helix: 1.07 (0.21), residues: 595 sheet: -1.13 (0.39), residues: 162 loop : -0.50 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 195 HIS 0.004 0.001 HIS A 180 PHE 0.027 0.002 PHE A 83 TYR 0.018 0.001 TYR B 426 ARG 0.010 0.001 ARG A 108 *********************** 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 282 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 253 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 HIS cc_start: 0.8206 (p90) cc_final: 0.8001 (p90) REVERT: A 81 GLU cc_start: 0.8055 (pp20) cc_final: 0.7785 (pp20) REVERT: A 157 ASN cc_start: 0.7194 (t0) cc_final: 0.6824 (t0) REVERT: A 162 ARG cc_start: 0.8382 (mtp180) cc_final: 0.7919 (mtp85) REVERT: A 205 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7473 (pp30) REVERT: A 286 MET cc_start: 0.7218 (mmm) cc_final: 0.6998 (mmp) REVERT: A 365 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7585 (pp20) REVERT: A 677 ASN cc_start: 0.8226 (t0) cc_final: 0.7967 (t0) REVERT: A 738 GLN cc_start: 0.8490 (mm-40) cc_final: 0.8115 (mm110) REVERT: A 740 ARG cc_start: 0.8176 (ttm-80) cc_final: 0.7864 (tpp80) REVERT: A 741 ARG cc_start: 0.8179 (ttp80) cc_final: 0.7620 (ttp-110) REVERT: A 745 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7895 (tpp) REVERT: A 882 LYS cc_start: 0.8337 (mmmt) cc_final: 0.7919 (mmmt) REVERT: B 386 ARG cc_start: 0.7023 (ttp-110) cc_final: 0.6726 (ttp-110) REVERT: B 452 TYR cc_start: 0.7756 (m-80) cc_final: 0.7413 (m-80) REVERT: B 496 GLU cc_start: 0.8583 (tp30) cc_final: 0.7845 (tp30) REVERT: B 499 GLN cc_start: 0.7436 (tm-30) cc_final: 0.6946 (tm-30) REVERT: B 535 ILE cc_start: 0.8750 (pt) cc_final: 0.8432 (pp) REVERT: B 540 ASP cc_start: 0.7791 (t0) cc_final: 0.7261 (t70) outliers start: 29 outliers final: 9 residues processed: 266 average time/residue: 1.1940 time to fit residues: 341.6882 Evaluate side-chains 248 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 236 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 478 GLN Chi-restraints excluded: chain B residue 550 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 0.8980 chunk 34 optimal weight: 0.3980 chunk 93 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 31 optimal weight: 0.9980 chunk 112 optimal weight: 20.0000 chunk 121 optimal weight: 4.9990 chunk 100 optimal weight: 9.9990 chunk 111 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 overall best weight: 2.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 HIS A 728 GLN 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: 0.7821 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10639 Z= 0.237 Angle : 0.592 9.725 14352 Z= 0.297 Chirality : 0.042 0.183 1551 Planarity : 0.004 0.035 1848 Dihedral : 4.544 53.344 1388 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.01 % Allowed : 17.48 % Favored : 79.50 % 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: 0.40 (0.24), residues: 1252 helix: 1.35 (0.21), residues: 596 sheet: -1.04 (0.40), residues: 147 loop : -0.55 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 195 HIS 0.005 0.001 HIS B 407 PHE 0.034 0.002 PHE B 456 TYR 0.017 0.001 TYR A 207 ARG 0.008 0.000 ARG A 382 *********************** 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 273 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 241 time to evaluate : 1.182 Fit side-chains REVERT: A 59 HIS cc_start: 0.8207 (p90) cc_final: 0.7993 (p90) REVERT: A 78 GLU cc_start: 0.7722 (pp20) cc_final: 0.7478 (pp20) REVERT: A 81 GLU cc_start: 0.7881 (pp20) cc_final: 0.6880 (pp20) REVERT: A 111 LYS cc_start: 0.8656 (mtpt) cc_final: 0.8342 (mttp) REVERT: A 157 ASN cc_start: 0.6924 (t0) cc_final: 0.6600 (t0) REVERT: A 205 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.7285 (pp30) REVERT: A 286 MET cc_start: 0.7101 (mmm) cc_final: 0.6881 (mmp) REVERT: A 382 ARG cc_start: 0.7946 (mmm160) cc_final: 0.7708 (tpt-90) REVERT: A 393 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8369 (mm) REVERT: A 677 ASN cc_start: 0.8234 (t0) cc_final: 0.7935 (t0) REVERT: A 741 ARG cc_start: 0.8270 (ttp80) cc_final: 0.7930 (ttm110) REVERT: A 745 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7861 (tpp) REVERT: A 765 ARG cc_start: 0.7688 (mtp85) cc_final: 0.6977 (mtt90) REVERT: A 809 GLN cc_start: 0.8078 (mp10) cc_final: 0.7766 (mp10) REVERT: A 825 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7531 (mp-120) REVERT: B 458 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8028 (pm20) REVERT: B 462 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8416 (mm-30) REVERT: B 496 GLU cc_start: 0.8576 (tp30) cc_final: 0.8295 (tp30) REVERT: B 499 GLN cc_start: 0.7438 (tm-30) cc_final: 0.7020 (tm-30) REVERT: B 525 MET cc_start: 0.7971 (mmp) cc_final: 0.7584 (mmp) REVERT: B 535 ILE cc_start: 0.8767 (pt) cc_final: 0.8451 (pp) REVERT: B 540 ASP cc_start: 0.7741 (t0) cc_final: 0.7249 (t70) REVERT: B 560 ASP cc_start: 0.8060 (t70) cc_final: 0.7839 (t70) outliers start: 32 outliers final: 12 residues processed: 252 average time/residue: 1.1111 time to fit residues: 303.1018 Evaluate side-chains 250 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 232 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 825 GLN Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 478 GLN Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 550 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 53 optimal weight: 0.0470 chunk 75 optimal weight: 6.9990 chunk 113 optimal weight: 9.9990 chunk 119 optimal weight: 20.0000 chunk 59 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 205 GLN ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 HIS A 958 GLN ** A1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 488 ASN ** 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: 0.7826 moved from start: 0.2223 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= 0.234 Angle : 0.587 9.685 14352 Z= 0.293 Chirality : 0.041 0.145 1551 Planarity : 0.004 0.040 1848 Dihedral : 4.323 39.227 1388 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.36 % Allowed : 18.69 % Favored : 77.95 % 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: 0.52 (0.24), residues: 1252 helix: 1.42 (0.21), residues: 601 sheet: -0.99 (0.41), residues: 145 loop : -0.47 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 195 HIS 0.004 0.001 HIS B 385 PHE 0.037 0.002 PHE B 456 TYR 0.016 0.001 TYR A 622 ARG 0.006 0.000 ARG A 741 *********************** 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 279 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 243 time to evaluate : 1.161 Fit side-chains revert: symmetry clash REVERT: A 78 GLU cc_start: 0.7674 (pp20) cc_final: 0.7449 (pp20) REVERT: A 81 GLU cc_start: 0.7879 (pp20) cc_final: 0.7343 (pp20) REVERT: A 83 PHE cc_start: 0.7691 (m-10) cc_final: 0.7488 (m-10) REVERT: A 109 GLU cc_start: 0.8112 (mp0) cc_final: 0.7835 (mp0) REVERT: A 157 ASN cc_start: 0.7235 (t0) cc_final: 0.6930 (t0) REVERT: A 172 GLU cc_start: 0.6939 (pp20) cc_final: 0.6537 (pp20) REVERT: A 205 GLN cc_start: 0.7678 (pt0) cc_final: 0.7256 (pp30) REVERT: A 382 ARG cc_start: 0.7955 (mmm160) cc_final: 0.7719 (tpt-90) REVERT: A 474 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7359 (mp0) REVERT: A 677 ASN cc_start: 0.8216 (t0) cc_final: 0.7921 (t0) REVERT: A 741 ARG cc_start: 0.8138 (ttp80) cc_final: 0.7936 (ttm110) REVERT: A 745 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7900 (tpp) REVERT: A 809 GLN cc_start: 0.8037 (mp10) cc_final: 0.7829 (mp10) REVERT: A 825 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7505 (mp-120) REVERT: A 852 ARG cc_start: 0.7879 (ptp90) cc_final: 0.7445 (mtm-85) REVERT: A 1010 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.6818 (mtp) REVERT: B 386 ARG cc_start: 0.7054 (ttp-110) cc_final: 0.6740 (ttp-110) REVERT: B 452 TYR cc_start: 0.7877 (m-80) cc_final: 0.7666 (m-80) REVERT: B 462 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8320 (mm-30) REVERT: B 496 GLU cc_start: 0.8604 (tp30) cc_final: 0.8316 (tp30) REVERT: B 499 GLN cc_start: 0.7472 (tm-30) cc_final: 0.7030 (tm-30) REVERT: B 525 MET cc_start: 0.8004 (mmp) cc_final: 0.7579 (mmp) REVERT: B 535 ILE cc_start: 0.8771 (pt) cc_final: 0.8448 (pp) REVERT: B 540 ASP cc_start: 0.7719 (t0) cc_final: 0.7257 (t70) outliers start: 36 outliers final: 13 residues processed: 259 average time/residue: 1.1389 time to fit residues: 318.1827 Evaluate side-chains 254 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 236 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 825 GLN Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1010 MET Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 478 GLN Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 550 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 102 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 0 optimal weight: 40.0000 chunk 61 optimal weight: 0.7980 chunk 107 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN A 450 HIS A 630 GLN 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: 0.7859 moved from start: 0.2516 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= 0.321 Angle : 0.629 9.750 14352 Z= 0.313 Chirality : 0.043 0.205 1551 Planarity : 0.004 0.040 1848 Dihedral : 4.328 25.422 1385 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.88 % Allowed : 19.04 % Favored : 77.09 % 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: 0.44 (0.24), residues: 1252 helix: 1.43 (0.21), residues: 598 sheet: -1.19 (0.41), residues: 143 loop : -0.56 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 479 HIS 0.004 0.001 HIS B 385 PHE 0.039 0.002 PHE B 456 TYR 0.021 0.002 TYR A 622 ARG 0.007 0.000 ARG B 348 *********************** 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 286 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 244 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.7673 (pp20) cc_final: 0.7282 (pp20) REVERT: A 81 GLU cc_start: 0.7829 (pp20) cc_final: 0.7305 (pp20) REVERT: A 109 GLU cc_start: 0.8131 (mp0) cc_final: 0.7855 (mp0) REVERT: A 110 GLU cc_start: 0.7849 (tp30) cc_final: 0.7113 (tp30) REVERT: A 157 ASN cc_start: 0.7219 (t0) cc_final: 0.6934 (t0) REVERT: A 205 GLN cc_start: 0.7730 (pt0) cc_final: 0.7422 (pp30) REVERT: A 206 LYS cc_start: 0.8998 (ptpp) cc_final: 0.8631 (ptpp) REVERT: A 263 GLU cc_start: 0.7644 (tp30) cc_final: 0.7424 (tp30) REVERT: A 286 MET cc_start: 0.7370 (mmp) cc_final: 0.7026 (mmp) REVERT: A 382 ARG cc_start: 0.8006 (mmm160) cc_final: 0.7722 (tpt-90) REVERT: A 393 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8580 (mm) REVERT: A 474 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7332 (mp0) REVERT: A 677 ASN cc_start: 0.8315 (t0) cc_final: 0.7960 (t0) REVERT: A 740 ARG cc_start: 0.8214 (ttm-80) cc_final: 0.7842 (tpp80) REVERT: A 745 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7921 (tpp) REVERT: A 852 ARG cc_start: 0.7831 (ptp90) cc_final: 0.7393 (mtm-85) REVERT: B 386 ARG cc_start: 0.7044 (ttp-110) cc_final: 0.6686 (ttp-110) REVERT: B 462 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8341 (mm-30) REVERT: B 496 GLU cc_start: 0.8633 (tp30) cc_final: 0.7890 (tp30) REVERT: B 499 GLN cc_start: 0.7554 (tm-30) cc_final: 0.7034 (tm-30) REVERT: B 525 MET cc_start: 0.8073 (mmp) cc_final: 0.7677 (mmp) REVERT: B 535 ILE cc_start: 0.8801 (pt) cc_final: 0.8458 (pp) REVERT: B 540 ASP cc_start: 0.7843 (t0) cc_final: 0.7391 (t70) outliers start: 42 outliers final: 17 residues processed: 266 average time/residue: 1.1848 time to fit residues: 339.8772 Evaluate side-chains 254 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 233 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 478 GLN Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 549 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 29 optimal weight: 0.0870 chunk 119 optimal weight: 20.0000 chunk 99 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- 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 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 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** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2542 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= 0.214 Angle : 0.609 10.419 14352 Z= 0.302 Chirality : 0.041 0.145 1551 Planarity : 0.004 0.040 1848 Dihedral : 4.240 28.748 1385 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.27 % Allowed : 20.84 % Favored : 75.88 % 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: 0.63 (0.24), residues: 1252 helix: 1.61 (0.21), residues: 591 sheet: -0.98 (0.42), residues: 145 loop : -0.50 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 479 HIS 0.005 0.001 HIS B 385 PHE 0.038 0.002 PHE B 456 TYR 0.021 0.001 TYR A 622 ARG 0.009 0.000 ARG B 348 *********************** 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 277 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 242 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.7664 (pp20) cc_final: 0.7400 (pp20) REVERT: A 87 ARG cc_start: 0.7840 (ttp-110) cc_final: 0.7635 (ttp-110) REVERT: A 109 GLU cc_start: 0.8086 (mp0) cc_final: 0.7788 (mp0) REVERT: A 111 LYS cc_start: 0.8690 (mtpt) cc_final: 0.8347 (mttp) REVERT: A 157 ASN cc_start: 0.7157 (t0) cc_final: 0.6897 (t0) REVERT: A 205 GLN cc_start: 0.7800 (pt0) cc_final: 0.7305 (pp30) REVERT: A 286 MET cc_start: 0.7325 (mmp) cc_final: 0.7076 (mmp) REVERT: A 393 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8438 (mm) REVERT: A 474 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7333 (mp0) REVERT: A 630 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.8065 (tt0) REVERT: A 677 ASN cc_start: 0.8170 (t0) cc_final: 0.7858 (t0) REVERT: A 740 ARG cc_start: 0.8248 (ttm-80) cc_final: 0.7899 (tpp80) REVERT: A 745 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.7876 (tpp) REVERT: A 852 ARG cc_start: 0.7803 (ptp90) cc_final: 0.7368 (mtm-85) REVERT: B 333 TRP cc_start: 0.8447 (p90) cc_final: 0.8246 (p90) REVERT: B 386 ARG cc_start: 0.6966 (ttp-110) cc_final: 0.6703 (ttp-110) REVERT: B 496 GLU cc_start: 0.8627 (tp30) cc_final: 0.7880 (tp30) REVERT: B 499 GLN cc_start: 0.7603 (tm-30) cc_final: 0.7092 (tm-30) REVERT: B 508 TYR cc_start: 0.6772 (t80) cc_final: 0.6467 (t80) REVERT: B 525 MET cc_start: 0.8054 (mmp) cc_final: 0.7669 (mmp) REVERT: B 535 ILE cc_start: 0.8803 (pt) cc_final: 0.8455 (pp) REVERT: B 540 ASP cc_start: 0.7816 (t0) cc_final: 0.7378 (t70) outliers start: 35 outliers final: 16 residues processed: 257 average time/residue: 1.2253 time to fit residues: 343.0574 Evaluate side-chains 248 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 228 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 630 GLN Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 478 GLN Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 581 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 8.9990 chunk 13 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 119 optimal weight: 30.0000 chunk 74 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 chunk 55 optimal weight: 0.7980 overall best weight: 4.9588 ------------------------------------------------------------------------------- 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 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN A 450 HIS A 630 GLN ** A 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 917 HIS ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 10639 Z= 0.366 Angle : 0.671 10.783 14352 Z= 0.334 Chirality : 0.044 0.180 1551 Planarity : 0.004 0.040 1848 Dihedral : 4.381 30.286 1385 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.45 % Allowed : 21.10 % Favored : 75.45 % 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: 0.39 (0.24), residues: 1252 helix: 1.39 (0.21), residues: 598 sheet: -1.19 (0.41), residues: 152 loop : -0.58 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 479 HIS 0.006 0.001 HIS B 385 PHE 0.037 0.003 PHE B 456 TYR 0.024 0.002 TYR A 622 ARG 0.008 0.001 ARG A 87 *********************** 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 273 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 236 time to evaluate : 1.323 Fit side-chains revert: symmetry clash REVERT: A 48 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7391 (pm20) REVERT: A 78 GLU cc_start: 0.7715 (pp20) cc_final: 0.7425 (pp20) REVERT: A 109 GLU cc_start: 0.8109 (mp0) cc_final: 0.7844 (mp0) REVERT: A 157 ASN cc_start: 0.7240 (t0) cc_final: 0.6977 (t0) REVERT: A 205 GLN cc_start: 0.7780 (pt0) cc_final: 0.7194 (pp30) REVERT: A 286 MET cc_start: 0.7428 (mmp) cc_final: 0.7181 (mmp) REVERT: A 382 ARG cc_start: 0.7951 (mmm160) cc_final: 0.7616 (tpt-90) REVERT: A 393 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8631 (mm) REVERT: A 474 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7305 (mp0) REVERT: A 677 ASN cc_start: 0.8199 (t0) cc_final: 0.7851 (t0) REVERT: A 740 ARG cc_start: 0.8255 (ttm-80) cc_final: 0.7923 (tpp80) REVERT: A 852 ARG cc_start: 0.7861 (ptp90) cc_final: 0.7419 (mtm-85) REVERT: B 386 ARG cc_start: 0.6958 (ttp-110) cc_final: 0.6677 (ttp-110) REVERT: B 496 GLU cc_start: 0.8647 (tp30) cc_final: 0.7909 (tp30) REVERT: B 499 GLN cc_start: 0.7611 (tm-30) cc_final: 0.7108 (tm-30) REVERT: B 525 MET cc_start: 0.8149 (mmp) cc_final: 0.7752 (mmp) REVERT: B 535 ILE cc_start: 0.8817 (pt) cc_final: 0.8461 (pp) REVERT: B 540 ASP cc_start: 0.7846 (t0) cc_final: 0.7448 (t70) outliers start: 37 outliers final: 18 residues processed: 255 average time/residue: 1.1466 time to fit residues: 317.4240 Evaluate side-chains 251 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 230 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 478 GLN Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 581 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 108 optimal weight: 0.0000 overall best weight: 0.6384 ------------------------------------------------------------------------------- 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 370 ASN A 444 ASN A 450 HIS A 630 GLN ** A 728 GLN ** 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: 0.7792 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10639 Z= 0.181 Angle : 0.631 11.275 14352 Z= 0.311 Chirality : 0.041 0.223 1551 Planarity : 0.004 0.038 1848 Dihedral : 4.248 31.937 1385 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.07 % Allowed : 23.00 % Favored : 74.94 % 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: 0.62 (0.24), residues: 1252 helix: 1.59 (0.21), residues: 595 sheet: -1.06 (0.43), residues: 147 loop : -0.47 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 479 HIS 0.006 0.001 HIS A 59 PHE 0.070 0.002 PHE A 83 TYR 0.019 0.001 TYR A 622 ARG 0.010 0.001 ARG A 87 *********************** 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 268 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 247 time to evaluate : 1.261 Fit side-chains revert: symmetry clash REVERT: A 59 HIS cc_start: 0.8221 (OUTLIER) cc_final: 0.7715 (p90) REVERT: A 83 PHE cc_start: 0.7905 (m-10) cc_final: 0.7672 (m-80) REVERT: A 87 ARG cc_start: 0.7915 (ttp-110) cc_final: 0.7674 (ttp-110) REVERT: A 109 GLU cc_start: 0.8029 (mp0) cc_final: 0.7814 (mp0) REVERT: A 157 ASN cc_start: 0.6923 (t0) cc_final: 0.6666 (t0) REVERT: A 205 GLN cc_start: 0.7767 (pt0) cc_final: 0.7231 (pp30) REVERT: A 286 MET cc_start: 0.7318 (mmp) cc_final: 0.7096 (mmp) REVERT: A 382 ARG cc_start: 0.7899 (mmm160) cc_final: 0.7574 (tpt-90) REVERT: A 474 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7271 (mp0) REVERT: A 677 ASN cc_start: 0.8131 (t0) cc_final: 0.7855 (t0) REVERT: A 733 LYS cc_start: 0.8865 (mttp) cc_final: 0.8581 (mtpp) REVERT: A 740 ARG cc_start: 0.8225 (ttm-80) cc_final: 0.7948 (tpp80) REVERT: A 765 ARG cc_start: 0.7701 (mtp85) cc_final: 0.7073 (mtt90) REVERT: A 852 ARG cc_start: 0.7784 (ptp90) cc_final: 0.7357 (mtm-85) REVERT: A 920 ASN cc_start: 0.8291 (p0) cc_final: 0.7961 (p0) REVERT: A 1037 GLU cc_start: 0.7754 (mp0) cc_final: 0.7455 (mp0) REVERT: B 367 ASP cc_start: 0.5919 (m-30) cc_final: 0.5562 (m-30) REVERT: B 386 ARG cc_start: 0.7038 (ttp-110) cc_final: 0.6755 (ttp-110) REVERT: B 425 LEU cc_start: 0.8585 (mt) cc_final: 0.8376 (mp) REVERT: B 489 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8450 (mm-30) REVERT: B 496 GLU cc_start: 0.8651 (tp30) cc_final: 0.7877 (tp30) REVERT: B 499 GLN cc_start: 0.7598 (tm-30) cc_final: 0.7060 (tm-30) REVERT: B 508 TYR cc_start: 0.6842 (t80) cc_final: 0.6501 (t80) REVERT: B 525 MET cc_start: 0.8067 (mmp) cc_final: 0.7698 (mmp) REVERT: B 535 ILE cc_start: 0.8812 (pt) cc_final: 0.8451 (pp) REVERT: B 540 ASP cc_start: 0.7808 (t0) cc_final: 0.7388 (t70) outliers start: 21 outliers final: 12 residues processed: 256 average time/residue: 1.1042 time to fit residues: 305.6809 Evaluate side-chains 242 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 228 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 478 GLN Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 597 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 20.0000 chunk 104 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 chunk 73 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 370 ASN A 450 HIS A 630 GLN A 728 GLN ** A 917 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 385 HIS ** 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: 0.7882 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 10639 Z= 0.445 Angle : 0.721 9.806 14352 Z= 0.360 Chirality : 0.046 0.225 1551 Planarity : 0.004 0.040 1848 Dihedral : 4.560 31.141 1385 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.10 % Allowed : 22.39 % Favored : 74.50 % 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: 0.38 (0.24), residues: 1252 helix: 1.42 (0.21), residues: 590 sheet: -1.25 (0.41), residues: 152 loop : -0.58 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 479 HIS 0.007 0.001 HIS B 385 PHE 0.072 0.003 PHE A 83 TYR 0.028 0.002 TYR A 622 ARG 0.010 0.001 ARG A 87 *********************** 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 260 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 227 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7450 (pm20) REVERT: A 59 HIS cc_start: 0.8128 (OUTLIER) cc_final: 0.7880 (p90) REVERT: A 109 GLU cc_start: 0.8110 (mp0) cc_final: 0.7860 (mp0) REVERT: A 110 GLU cc_start: 0.7870 (tp30) cc_final: 0.7138 (tp30) REVERT: A 157 ASN cc_start: 0.7338 (t0) cc_final: 0.7071 (t0) REVERT: A 172 GLU cc_start: 0.7175 (pp20) cc_final: 0.6960 (pp20) REVERT: A 205 GLN cc_start: 0.7812 (pt0) cc_final: 0.7229 (pp30) REVERT: A 278 MET cc_start: 0.7425 (mmt) cc_final: 0.7115 (mmp) REVERT: A 286 MET cc_start: 0.7420 (mmp) cc_final: 0.7181 (mmp) REVERT: A 382 ARG cc_start: 0.8008 (mmm160) cc_final: 0.7687 (tpt-90) REVERT: A 393 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8623 (mm) REVERT: A 474 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7364 (mp0) REVERT: A 677 ASN cc_start: 0.8215 (t0) cc_final: 0.7838 (t0) REVERT: A 728 GLN cc_start: 0.7434 (OUTLIER) cc_final: 0.6634 (tp40) REVERT: A 733 LYS cc_start: 0.8876 (mttp) cc_final: 0.8594 (mtpp) REVERT: A 740 ARG cc_start: 0.8210 (ttm-80) cc_final: 0.7931 (tpp80) REVERT: A 809 GLN cc_start: 0.8102 (mp10) cc_final: 0.7407 (mp10) REVERT: A 852 ARG cc_start: 0.7852 (ptp90) cc_final: 0.7430 (mtm-85) REVERT: A 920 ASN cc_start: 0.8418 (p0) cc_final: 0.8052 (p0) REVERT: A 1037 GLU cc_start: 0.7889 (mp0) cc_final: 0.7564 (mp0) REVERT: B 329 GLN cc_start: 0.8548 (tp-100) cc_final: 0.8066 (tp-100) REVERT: B 386 ARG cc_start: 0.6994 (ttp-110) cc_final: 0.6698 (ttp-110) REVERT: B 425 LEU cc_start: 0.8566 (mt) cc_final: 0.8362 (mp) REVERT: B 491 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8910 (mp) REVERT: B 496 GLU cc_start: 0.8674 (tp30) cc_final: 0.7955 (tp30) REVERT: B 499 GLN cc_start: 0.7646 (tm-30) cc_final: 0.7142 (tm-30) REVERT: B 525 MET cc_start: 0.8165 (mmp) cc_final: 0.7777 (mmp) REVERT: B 535 ILE cc_start: 0.8829 (pt) cc_final: 0.8454 (pp) REVERT: B 540 ASP cc_start: 0.7848 (t0) cc_final: 0.7474 (t70) outliers start: 33 outliers final: 12 residues processed: 245 average time/residue: 1.1783 time to fit residues: 312.1064 Evaluate side-chains 240 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 222 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 728 GLN Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 478 GLN Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 597 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 20.0000 chunk 71 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 123 optimal weight: 8.9990 chunk 113 optimal weight: 20.0000 chunk 98 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 450 HIS A 630 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: 0.7880 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.195 10639 Z= 0.496 Angle : 1.066 59.095 14352 Z= 0.605 Chirality : 0.049 0.667 1551 Planarity : 0.007 0.218 1848 Dihedral : 4.585 30.501 1385 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.07 % Allowed : 23.43 % Favored : 74.50 % Cbeta Deviations : 0.17 % 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: 0.35 (0.24), residues: 1252 helix: 1.42 (0.21), residues: 590 sheet: -1.26 (0.41), residues: 152 loop : -0.63 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 479 HIS 0.370 0.008 HIS A 59 PHE 0.043 0.003 PHE A 83 TYR 0.024 0.002 TYR A 622 ARG 0.009 0.001 ARG A 87 ********************** 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 243 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 222 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7449 (pm20) REVERT: A 109 GLU cc_start: 0.8102 (mp0) cc_final: 0.7857 (mp0) REVERT: A 110 GLU cc_start: 0.7866 (tp30) cc_final: 0.7151 (tp30) REVERT: A 157 ASN cc_start: 0.7337 (t0) cc_final: 0.7070 (t0) REVERT: A 172 GLU cc_start: 0.7174 (pp20) cc_final: 0.6954 (pp20) REVERT: A 205 GLN cc_start: 0.7839 (pt0) cc_final: 0.7229 (pp30) REVERT: A 278 MET cc_start: 0.7427 (mmt) cc_final: 0.7119 (mmp) REVERT: A 286 MET cc_start: 0.7424 (mmp) cc_final: 0.7167 (mmp) REVERT: A 382 ARG cc_start: 0.8005 (mmm160) cc_final: 0.7687 (tpt-90) REVERT: A 393 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8619 (mm) REVERT: A 474 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7362 (mp0) REVERT: A 677 ASN cc_start: 0.8198 (t0) cc_final: 0.7826 (t0) REVERT: A 733 LYS cc_start: 0.8881 (mttp) cc_final: 0.8598 (mtpp) REVERT: A 740 ARG cc_start: 0.8206 (ttm-80) cc_final: 0.7932 (tpp80) REVERT: A 852 ARG cc_start: 0.7849 (ptp90) cc_final: 0.7429 (mtm-85) REVERT: A 920 ASN cc_start: 0.8417 (p0) cc_final: 0.8046 (p0) REVERT: A 1037 GLU cc_start: 0.7886 (mp0) cc_final: 0.7651 (mp0) REVERT: B 329 GLN cc_start: 0.8555 (tp-100) cc_final: 0.8065 (tp-100) REVERT: B 386 ARG cc_start: 0.6992 (ttp-110) cc_final: 0.6694 (ttp-110) REVERT: B 425 LEU cc_start: 0.8566 (mt) cc_final: 0.8361 (mp) REVERT: B 491 ILE cc_start: 0.9111 (OUTLIER) cc_final: 0.8909 (mp) REVERT: B 496 GLU cc_start: 0.8673 (tp30) cc_final: 0.7955 (tp30) REVERT: B 499 GLN cc_start: 0.7646 (tm-30) cc_final: 0.7140 (tm-30) REVERT: B 508 TYR cc_start: 0.6953 (t80) cc_final: 0.6554 (t80) REVERT: B 525 MET cc_start: 0.8165 (mmp) cc_final: 0.7776 (mmp) REVERT: B 535 ILE cc_start: 0.8829 (pt) cc_final: 0.8453 (pp) REVERT: B 540 ASP cc_start: 0.7846 (t0) cc_final: 0.7474 (t70) outliers start: 21 outliers final: 14 residues processed: 234 average time/residue: 1.1203 time to fit residues: 284.2927 Evaluate side-chains 236 residues out of total 1141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 218 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 478 GLN Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 597 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 101 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 450 HIS A 630 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.165385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.107569 restraints weight = 21542.072| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 3.49 r_work: 0.3069 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3075 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.195 10639 Z= 0.496 Angle : 1.066 59.094 14352 Z= 0.605 Chirality : 0.049 0.667 1551 Planarity : 0.007 0.218 1848 Dihedral : 4.585 30.501 1385 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.89 % Allowed : 23.60 % Favored : 74.50 % Cbeta Deviations : 0.17 % 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: 0.35 (0.24), residues: 1252 helix: 1.42 (0.21), residues: 590 sheet: -1.26 (0.41), residues: 152 loop : -0.63 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 479 HIS 0.370 0.008 HIS A 59 PHE 0.043 0.003 PHE A 83 TYR 0.024 0.002 TYR A 622 ARG 0.009 0.001 ARG A 87 =============================================================================== Job complete usr+sys time: 5033.09 seconds wall clock time: 89 minutes 56.77 seconds (5396.77 seconds total)