Starting phenix.real_space_refine on Mon Mar 11 09:06:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w7v_32349/03_2024/7w7v_32349_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w7v_32349/03_2024/7w7v_32349.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w7v_32349/03_2024/7w7v_32349.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w7v_32349/03_2024/7w7v_32349.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w7v_32349/03_2024/7w7v_32349_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w7v_32349/03_2024/7w7v_32349_updated.pdb" } resolution = 3.0 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.009 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: 7 Type Number sf(0) Gaussians Mg 1 5.21 5 S 58 5.16 5 Be 1 3.05 5 C 4984 2.51 5 N 1305 2.21 5 O 1471 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 144": "OD1" <-> "OD2" Residue "A GLU 152": "OE1" <-> "OE2" Residue "A ASP 176": "OD1" <-> "OD2" Residue "A ASP 237": "OD1" <-> "OD2" Residue "A PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A GLU 394": "OE1" <-> "OE2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A PHE 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 694": "OD1" <-> "OD2" Residue "A PHE 944": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 980": "OD1" <-> "OD2" Residue "A GLU 981": "OE1" <-> "OE2" Residue "A PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1033": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7823 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1014, 7823 Unusual residues: {' MG': 1, 'BEF': 1} Classifications: {'peptide': 1012, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 45, 'TRANS': 966, None: 2} Not linked: pdbres="SER A1042 " pdbres="BEF A2001 " Not linked: pdbres="BEF A2001 " pdbres=" MG A2002 " Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 4.63, per 1000 atoms: 0.59 Number of scatterers: 7823 At special positions: 0 Unit cell: (88.395, 98.355, 141.93, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 58 16.00 Mg 1 11.99 F 3 9.00 O 1471 8.00 N 1305 7.00 C 4984 6.00 Be 1 4.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.13 Conformation dependent library (CDL) restraints added in 1.3 seconds 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1896 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 39 helices and 8 sheets defined 48.3% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'A' and resid 9 through 16 removed outlier: 3.623A pdb=" N PHE A 16 " --> pdb=" O VAL A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 36 Processing helix chain 'A' and resid 49 through 58 removed outlier: 3.827A pdb=" N PHE A 57 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N GLU A 58 " --> pdb=" O ILE A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 78 Processing helix chain 'A' and resid 85 through 119 Proline residue: A 91 - end of helix removed outlier: 3.836A pdb=" N LEU A 96 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ASN A 101 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLN A 108 " --> pdb=" O GLY A 105 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N GLU A 117 " --> pdb=" O ASN A 114 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALA A 118 " --> pdb=" O ALA A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 144 No H-bonds generated for 'chain 'A' and resid 142 through 144' Processing helix chain 'A' and resid 178 through 181 No H-bonds generated for 'chain 'A' and resid 178 through 181' Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 231 through 241 Processing helix chain 'A' and resid 248 through 275 Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 292 through 306 Processing helix chain 'A' and resid 311 through 328 Processing helix chain 'A' and resid 336 through 339 Processing helix chain 'A' and resid 404 through 406 No H-bonds generated for 'chain 'A' and resid 404 through 406' Processing helix chain 'A' and resid 408 through 420 Processing helix chain 'A' and resid 440 through 451 Processing helix chain 'A' and resid 464 through 467 No H-bonds generated for 'chain 'A' and resid 464 through 467' Processing helix chain 'A' and resid 470 through 478 removed outlier: 3.938A pdb=" N VAL A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 522 Processing helix chain 'A' and resid 538 through 552 Processing helix chain 'A' and resid 581 through 587 removed outlier: 4.073A pdb=" N LYS A 585 " --> pdb=" O ALA A 581 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU A 587 " --> pdb=" O PHE A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 615 Processing helix chain 'A' and resid 628 through 638 Processing helix chain 'A' and resid 654 through 659 Processing helix chain 'A' and resid 662 through 671 removed outlier: 3.916A pdb=" N ASP A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 693 removed outlier: 3.736A pdb=" N PHE A 693 " --> pdb=" O PHE A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 712 Proline residue: A 708 - end of helix Processing helix chain 'A' and resid 724 through 729 Processing helix chain 'A' and resid 739 through 780 removed outlier: 3.579A pdb=" N LEU A 780 " --> pdb=" O THR A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 808 removed outlier: 4.331A pdb=" N ASP A 799 " --> pdb=" O ASN A 795 " (cutoff:3.500A) Proline residue: A 802 - end of helix removed outlier: 3.609A pdb=" N PHE A 808 " --> pdb=" O THR A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 856 Processing helix chain 'A' and resid 888 through 891 Processing helix chain 'A' and resid 893 through 912 Processing helix chain 'A' and resid 926 through 928 No H-bonds generated for 'chain 'A' and resid 926 through 928' Processing helix chain 'A' and resid 930 through 947 Processing helix chain 'A' and resid 952 through 955 No H-bonds generated for 'chain 'A' and resid 952 through 955' Processing helix chain 'A' and resid 963 through 989 Proline residue: A 975 - end of helix removed outlier: 3.861A pdb=" N LEU A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1031 removed outlier: 3.589A pdb=" N LEU A1021 " --> pdb=" O PRO A1017 " (cutoff:3.500A) Proline residue: A1024 - end of helix removed outlier: 4.690A pdb=" N TRP A1028 " --> pdb=" O PRO A1024 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER A1031 " --> pdb=" O ILE A1027 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 126 through 129 Processing sheet with id= B, first strand: chain 'A' and resid 150 through 153 removed outlier: 7.071A pdb=" N ASP A 162 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 173 through 175 removed outlier: 4.594A pdb=" N LEU A 173 " --> pdb=" O LYS A 189 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 331 through 333 removed outlier: 6.821A pdb=" N VAL A 347 " --> pdb=" O ALA A 698 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N THR A 700 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N CYS A 349 " --> pdb=" O THR A 700 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ARG A 619 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N SER A 350 " --> pdb=" O ARG A 619 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE A 621 " --> pdb=" O SER A 350 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 425 through 428 Processing sheet with id= F, first strand: chain 'A' and resid 376 through 383 removed outlier: 3.600A pdb=" N THR A 376 " --> pdb=" O GLU A 373 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ASN A 380 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N LEU A 369 " --> pdb=" O ASN A 380 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N PHE A 382 " --> pdb=" O PHE A 367 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N PHE A 367 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLY A 597 " --> pdb=" O CYS A 364 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N MET A 366 " --> pdb=" O CYS A 595 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N CYS A 595 " --> pdb=" O MET A 366 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N ILE A 368 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 9.287A pdb=" N VAL A 593 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 12.467A pdb=" N ASP A 370 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 15.579A pdb=" N THR A 591 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LEU A 563 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N CYS A 595 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU A 561 " --> pdb=" O CYS A 595 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLY A 597 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ARG A 559 " --> pdb=" O GLY A 597 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N THR A 499 " --> pdb=" O LYS A 481 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LYS A 481 " --> pdb=" O THR A 499 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 527 through 529 Processing sheet with id= H, first strand: chain 'A' and resid 651 through 653 removed outlier: 6.385A pdb=" N CYS A 674 " --> pdb=" O PHE A 652 " (cutoff:3.500A) No H-bonds generated for sheet with id= H 362 hydrogen bonds defined for protein. 855 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.78 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2554 1.34 - 1.46: 1500 1.46 - 1.58: 3824 1.58 - 1.70: 0 1.70 - 1.82: 90 Bond restraints: 7968 Sorted by residual: bond pdb=" BE BEF A2001 " pdb=" F2 BEF A2001 " ideal model delta sigma weight residual 1.476 1.560 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" BE BEF A2001 " pdb=" F3 BEF A2001 " ideal model delta sigma weight residual 1.476 1.546 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" BE BEF A2001 " pdb=" F1 BEF A2001 " ideal model delta sigma weight residual 1.476 1.534 -0.058 2.00e-02 2.50e+03 8.32e+00 bond pdb=" C MET A1023 " pdb=" N PRO A1024 " ideal model delta sigma weight residual 1.337 1.351 -0.014 9.80e-03 1.04e+04 2.18e+00 bond pdb=" CB GLU A 748 " pdb=" CG GLU A 748 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 9.79e-01 ... (remaining 7963 not shown) Histogram of bond angle deviations from ideal: 99.03 - 106.02: 197 106.02 - 113.01: 4426 113.01 - 120.00: 2639 120.00 - 126.99: 3462 126.99 - 133.98: 89 Bond angle restraints: 10813 Sorted by residual: angle pdb=" F2 BEF A2001 " pdb=" BE BEF A2001 " pdb=" F3 BEF A2001 " ideal model delta sigma weight residual 119.96 106.30 13.66 3.00e+00 1.11e-01 2.07e+01 angle pdb=" F1 BEF A2001 " pdb=" BE BEF A2001 " pdb=" F3 BEF A2001 " ideal model delta sigma weight residual 120.12 109.90 10.22 3.00e+00 1.11e-01 1.16e+01 angle pdb=" N GLY A 291 " pdb=" CA GLY A 291 " pdb=" C GLY A 291 " ideal model delta sigma weight residual 115.66 110.50 5.16 1.56e+00 4.11e-01 1.09e+01 angle pdb=" F1 BEF A2001 " pdb=" BE BEF A2001 " pdb=" F2 BEF A2001 " ideal model delta sigma weight residual 119.91 112.04 7.87 3.00e+00 1.11e-01 6.88e+00 angle pdb=" C GLN A 758 " pdb=" N PHE A 759 " pdb=" CA PHE A 759 " ideal model delta sigma weight residual 121.14 116.57 4.57 1.75e+00 3.27e-01 6.81e+00 ... (remaining 10808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 4388 17.45 - 34.91: 365 34.91 - 52.36: 54 52.36 - 69.81: 8 69.81 - 87.27: 10 Dihedral angle restraints: 4825 sinusoidal: 1901 harmonic: 2924 Sorted by residual: dihedral pdb=" CA MET A 536 " pdb=" C MET A 536 " pdb=" N THR A 537 " pdb=" CA THR A 537 " ideal model delta harmonic sigma weight residual 180.00 161.40 18.60 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CB GLU A 439 " pdb=" CG GLU A 439 " pdb=" CD GLU A 439 " pdb=" OE1 GLU A 439 " ideal model delta sinusoidal sigma weight residual 0.00 86.67 -86.67 1 3.00e+01 1.11e-03 1.00e+01 dihedral pdb=" CA GLU A 950 " pdb=" C GLU A 950 " pdb=" N PRO A 951 " pdb=" CA PRO A 951 " ideal model delta harmonic sigma weight residual -180.00 -164.86 -15.14 0 5.00e+00 4.00e-02 9.16e+00 ... (remaining 4822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 862 0.036 - 0.072: 288 0.072 - 0.109: 95 0.109 - 0.145: 22 0.145 - 0.181: 2 Chirality restraints: 1269 Sorted by residual: chirality pdb=" CA PHE A 759 " pdb=" N PHE A 759 " pdb=" C PHE A 759 " pdb=" CB PHE A 759 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.21e-01 chirality pdb=" CA GLU A 90 " pdb=" N GLU A 90 " pdb=" C GLU A 90 " pdb=" CB GLU A 90 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" CA LEU A 974 " pdb=" N LEU A 974 " pdb=" C LEU A 974 " pdb=" CB LEU A 974 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.27e-01 ... (remaining 1266 not shown) Planarity restraints: 1378 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 534 " -0.065 5.00e-02 4.00e+02 9.88e-02 1.56e+01 pdb=" N PRO A 535 " 0.171 5.00e-02 4.00e+02 pdb=" CA PRO A 535 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 535 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 796 " 0.009 2.00e-02 2.50e+03 1.71e-02 2.94e+00 pdb=" C LEU A 796 " -0.030 2.00e-02 2.50e+03 pdb=" O LEU A 796 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL A 797 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 759 " -0.011 2.00e-02 2.50e+03 1.04e-02 1.90e+00 pdb=" CG PHE A 759 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE A 759 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 759 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 759 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 759 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 759 " -0.004 2.00e-02 2.50e+03 ... (remaining 1375 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 73 2.59 - 3.17: 6846 3.17 - 3.74: 12814 3.74 - 4.32: 17077 4.32 - 4.90: 27930 Nonbonded interactions: 64740 Sorted by model distance: nonbonded pdb=" OD2 ASP A 351 " pdb=" F3 BEF A2001 " model vdw 2.010 2.390 nonbonded pdb=" OD2 ASP A 351 " pdb="MG MG A2002 " model vdw 2.064 2.170 nonbonded pdb=" O THR A 353 " pdb="MG MG A2002 " model vdw 2.064 2.170 nonbonded pdb=" OD1 ASP A 702 " pdb="MG MG A2002 " model vdw 2.076 2.170 nonbonded pdb=" OE2 GLU A 373 " pdb=" OG1 THR A 376 " model vdw 2.130 2.440 ... (remaining 64735 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=1.00 max=1.00 mean=1.00 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: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.430 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 24.790 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 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 0.084 7968 Z= 0.150 Angle : 0.555 13.660 10813 Z= 0.299 Chirality : 0.041 0.181 1269 Planarity : 0.004 0.099 1378 Dihedral : 13.316 87.266 2929 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.27), residues: 1006 helix: 1.34 (0.24), residues: 483 sheet: -0.15 (0.51), residues: 97 loop : -0.44 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 831 HIS 0.009 0.001 HIS A 278 PHE 0.024 0.001 PHE A 759 TYR 0.007 0.001 TYR A 842 ARG 0.004 0.000 ARG A 666 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 0.869 Fit side-chains revert: symmetry clash REVERT: A 8 THR cc_start: 0.7687 (p) cc_final: 0.7479 (t) REVERT: A 207 MET cc_start: 0.8443 (mmm) cc_final: 0.7943 (mmm) REVERT: A 218 LYS cc_start: 0.8225 (ttmt) cc_final: 0.7872 (ttmt) REVERT: A 238 GLU cc_start: 0.6968 (tt0) cc_final: 0.6700 (tt0) REVERT: A 259 GLN cc_start: 0.5474 (mt0) cc_final: 0.5268 (mt0) REVERT: A 361 MET cc_start: 0.8148 (tpp) cc_final: 0.7754 (tpp) REVERT: A 437 VAL cc_start: 0.6945 (m) cc_final: 0.6724 (t) REVERT: A 452 MET cc_start: 0.8382 (ptt) cc_final: 0.8095 (ptt) REVERT: A 466 GLU cc_start: 0.6981 (pm20) cc_final: 0.6280 (tp30) REVERT: A 487 PHE cc_start: 0.6587 (t80) cc_final: 0.6231 (t80) REVERT: A 508 MET cc_start: 0.5266 (tmm) cc_final: 0.3693 (tpp) REVERT: A 536 MET cc_start: 0.3243 (mmp) cc_final: 0.2114 (tpp) REVERT: A 670 LEU cc_start: 0.7702 (mm) cc_final: 0.7441 (mt) REVERT: A 699 MET cc_start: 0.8088 (tpt) cc_final: 0.5974 (tpt) REVERT: A 824 LYS cc_start: 0.7183 (mmtt) cc_final: 0.6570 (mmpt) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 1.1764 time to fit residues: 205.5407 Evaluate side-chains 112 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.2980 chunk 76 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 chunk 79 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN A 428 ASN A 477 GLN A 918 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7968 Z= 0.165 Angle : 0.510 10.152 10813 Z= 0.267 Chirality : 0.041 0.163 1269 Planarity : 0.005 0.075 1378 Dihedral : 3.881 17.239 1070 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.08 % Allowed : 11.46 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.27), residues: 1006 helix: 1.01 (0.24), residues: 487 sheet: -0.25 (0.52), residues: 94 loop : -0.39 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 927 HIS 0.007 0.001 HIS A 405 PHE 0.021 0.001 PHE A 759 TYR 0.013 0.001 TYR A 497 ARG 0.005 0.000 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 116 time to evaluate : 0.777 Fit side-chains revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7193 (tptp) REVERT: A 157 ASP cc_start: 0.7208 (OUTLIER) cc_final: 0.6425 (m-30) REVERT: A 218 LYS cc_start: 0.8210 (ttmt) cc_final: 0.7893 (ttmt) REVERT: A 238 GLU cc_start: 0.7000 (tt0) cc_final: 0.6730 (tt0) REVERT: A 259 GLN cc_start: 0.5787 (mt0) cc_final: 0.5411 (mt0) REVERT: A 413 LEU cc_start: 0.7887 (tp) cc_final: 0.7466 (tt) REVERT: A 439 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.6465 (tm-30) REVERT: A 452 MET cc_start: 0.8374 (ptt) cc_final: 0.8095 (ptt) REVERT: A 466 GLU cc_start: 0.7113 (pm20) cc_final: 0.6392 (tp30) REVERT: A 487 PHE cc_start: 0.6588 (t80) cc_final: 0.6234 (t80) REVERT: A 508 MET cc_start: 0.5284 (tmm) cc_final: 0.3626 (tpp) REVERT: A 536 MET cc_start: 0.3548 (mmp) cc_final: 0.2591 (tpp) REVERT: A 670 LEU cc_start: 0.7631 (mm) cc_final: 0.7209 (mt) REVERT: A 699 MET cc_start: 0.8092 (tpt) cc_final: 0.5875 (tpt) REVERT: A 731 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6613 (mt-10) REVERT: A 824 LYS cc_start: 0.7229 (mmtt) cc_final: 0.6638 (mmpt) REVERT: A 1023 MET cc_start: 0.2981 (tmt) cc_final: 0.2343 (ptt) outliers start: 18 outliers final: 8 residues processed: 127 average time/residue: 1.1676 time to fit residues: 157.6383 Evaluate side-chains 116 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 104 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 595 CYS Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 669 CYS Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 916 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 81 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN A 918 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7968 Z= 0.168 Angle : 0.484 6.529 10813 Z= 0.257 Chirality : 0.041 0.162 1269 Planarity : 0.005 0.062 1378 Dihedral : 3.900 18.087 1070 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.01 % Allowed : 12.27 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.26), residues: 1006 helix: 0.86 (0.24), residues: 489 sheet: -0.46 (0.51), residues: 96 loop : -0.38 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 927 HIS 0.002 0.000 HIS A 943 PHE 0.024 0.001 PHE A 759 TYR 0.010 0.001 TYR A 497 ARG 0.003 0.000 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 111 time to evaluate : 0.859 Fit side-chains REVERT: A 33 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7328 (tptp) REVERT: A 157 ASP cc_start: 0.7199 (OUTLIER) cc_final: 0.6432 (m-30) REVERT: A 207 MET cc_start: 0.8385 (mmm) cc_final: 0.7952 (mmm) REVERT: A 218 LYS cc_start: 0.8214 (ttmt) cc_final: 0.7909 (ttmt) REVERT: A 238 GLU cc_start: 0.7075 (tt0) cc_final: 0.6752 (tt0) REVERT: A 259 GLN cc_start: 0.5852 (mt0) cc_final: 0.5515 (mt0) REVERT: A 413 LEU cc_start: 0.7905 (tp) cc_final: 0.7448 (tt) REVERT: A 439 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6657 (tm-30) REVERT: A 452 MET cc_start: 0.8448 (ptt) cc_final: 0.8114 (ptt) REVERT: A 466 GLU cc_start: 0.7197 (pm20) cc_final: 0.6384 (tp30) REVERT: A 487 PHE cc_start: 0.6626 (t80) cc_final: 0.6254 (t80) REVERT: A 508 MET cc_start: 0.5382 (tmm) cc_final: 0.3630 (tpp) REVERT: A 536 MET cc_start: 0.3702 (mmp) cc_final: 0.2919 (tpt) REVERT: A 575 MET cc_start: 0.3398 (mmp) cc_final: 0.2499 (ppp) REVERT: A 699 MET cc_start: 0.8139 (tpt) cc_final: 0.5896 (tpt) REVERT: A 731 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6622 (mt-10) REVERT: A 824 LYS cc_start: 0.7226 (mmtt) cc_final: 0.6624 (mmpt) REVERT: A 1023 MET cc_start: 0.3301 (tmt) cc_final: 0.2462 (ptt) REVERT: A 1039 MET cc_start: 0.3111 (mmm) cc_final: 0.2811 (mmm) outliers start: 26 outliers final: 12 residues processed: 128 average time/residue: 1.1289 time to fit residues: 153.8973 Evaluate side-chains 116 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 595 CYS Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 669 CYS Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 764 ILE Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 916 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 ASN A 918 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7968 Z= 0.207 Angle : 0.511 6.405 10813 Z= 0.271 Chirality : 0.042 0.170 1269 Planarity : 0.005 0.056 1378 Dihedral : 4.033 20.351 1070 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.36 % Allowed : 14.00 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.26), residues: 1006 helix: 0.65 (0.24), residues: 493 sheet: -0.61 (0.48), residues: 91 loop : -0.44 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 927 HIS 0.004 0.001 HIS A 405 PHE 0.027 0.001 PHE A 759 TYR 0.010 0.001 TYR A 990 ARG 0.003 0.000 ARG A 923 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 111 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6118 (tpp) cc_final: 0.5885 (tpp) REVERT: A 33 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7315 (tptp) REVERT: A 157 ASP cc_start: 0.7423 (OUTLIER) cc_final: 0.6693 (m-30) REVERT: A 207 MET cc_start: 0.8409 (mmm) cc_final: 0.7948 (mmm) REVERT: A 218 LYS cc_start: 0.8214 (ttmt) cc_final: 0.7923 (ttmt) REVERT: A 228 VAL cc_start: 0.8200 (t) cc_final: 0.7958 (m) REVERT: A 238 GLU cc_start: 0.7096 (tt0) cc_final: 0.6765 (tt0) REVERT: A 250 GLN cc_start: 0.7304 (mt0) cc_final: 0.7097 (mt0) REVERT: A 259 GLN cc_start: 0.5931 (mt0) cc_final: 0.5631 (mt0) REVERT: A 384 ILE cc_start: 0.8214 (mm) cc_final: 0.7775 (mp) REVERT: A 413 LEU cc_start: 0.8017 (tp) cc_final: 0.7470 (tt) REVERT: A 439 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6610 (tm-30) REVERT: A 452 MET cc_start: 0.8453 (ptt) cc_final: 0.8121 (ptt) REVERT: A 466 GLU cc_start: 0.7291 (pm20) cc_final: 0.6406 (tp30) REVERT: A 487 PHE cc_start: 0.6590 (t80) cc_final: 0.6217 (t80) REVERT: A 508 MET cc_start: 0.5280 (tmm) cc_final: 0.3361 (tpp) REVERT: A 536 MET cc_start: 0.3860 (mmp) cc_final: 0.3241 (tpt) REVERT: A 575 MET cc_start: 0.3337 (mmp) cc_final: 0.2242 (ppp) REVERT: A 699 MET cc_start: 0.8136 (tpt) cc_final: 0.5983 (tpt) REVERT: A 731 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6613 (mp0) REVERT: A 824 LYS cc_start: 0.7228 (mmtt) cc_final: 0.6643 (mmpt) REVERT: A 1023 MET cc_start: 0.3774 (tmt) cc_final: 0.2847 (ptt) outliers start: 29 outliers final: 14 residues processed: 130 average time/residue: 1.1401 time to fit residues: 157.7858 Evaluate side-chains 125 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 107 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 595 CYS Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 669 CYS Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 916 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 767 ASN A 918 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7968 Z= 0.330 Angle : 0.575 6.048 10813 Z= 0.306 Chirality : 0.045 0.195 1269 Planarity : 0.006 0.051 1378 Dihedral : 4.444 22.782 1070 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.28 % Allowed : 15.05 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.26), residues: 1006 helix: 0.23 (0.23), residues: 488 sheet: -1.00 (0.48), residues: 95 loop : -0.50 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 927 HIS 0.004 0.001 HIS A 943 PHE 0.031 0.002 PHE A 759 TYR 0.012 0.002 TYR A 836 ARG 0.003 0.001 ARG A 750 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 108 time to evaluate : 0.881 Fit side-chains revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7429 (tptp) REVERT: A 157 ASP cc_start: 0.7546 (OUTLIER) cc_final: 0.6775 (m-30) REVERT: A 207 MET cc_start: 0.8453 (mmm) cc_final: 0.8053 (mmm) REVERT: A 218 LYS cc_start: 0.8245 (ttmt) cc_final: 0.7994 (ttmt) REVERT: A 238 GLU cc_start: 0.7148 (tt0) cc_final: 0.6719 (tt0) REVERT: A 259 GLN cc_start: 0.6044 (mt0) cc_final: 0.5666 (mt0) REVERT: A 380 ASN cc_start: 0.7868 (OUTLIER) cc_final: 0.7584 (m110) REVERT: A 384 ILE cc_start: 0.8313 (mm) cc_final: 0.7933 (mp) REVERT: A 413 LEU cc_start: 0.8109 (tp) cc_final: 0.7593 (tt) REVERT: A 439 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6928 (tm-30) REVERT: A 452 MET cc_start: 0.8508 (ptt) cc_final: 0.8189 (ptt) REVERT: A 466 GLU cc_start: 0.7444 (pm20) cc_final: 0.6564 (tp30) REVERT: A 487 PHE cc_start: 0.6586 (t80) cc_final: 0.6180 (t80) REVERT: A 536 MET cc_start: 0.3815 (mmp) cc_final: 0.3320 (tpt) REVERT: A 575 MET cc_start: 0.3014 (mmp) cc_final: 0.2752 (mmt) REVERT: A 699 MET cc_start: 0.8088 (tpt) cc_final: 0.5849 (tpt) REVERT: A 731 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.6289 (mp0) REVERT: A 756 MET cc_start: 0.7227 (OUTLIER) cc_final: 0.6896 (mtp) REVERT: A 824 LYS cc_start: 0.7249 (mmtt) cc_final: 0.6645 (mmpt) REVERT: A 917 GLU cc_start: 0.7649 (tp30) cc_final: 0.7346 (tp30) REVERT: A 1023 MET cc_start: 0.3648 (tmt) cc_final: 0.2710 (ptt) outliers start: 37 outliers final: 21 residues processed: 136 average time/residue: 1.1063 time to fit residues: 160.0962 Evaluate side-chains 135 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 108 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 595 CYS Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 669 CYS Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 764 ILE Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 916 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.0670 chunk 19 optimal weight: 0.6980 chunk 57 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 918 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7968 Z= 0.153 Angle : 0.480 6.842 10813 Z= 0.254 Chirality : 0.041 0.167 1269 Planarity : 0.005 0.051 1378 Dihedral : 4.020 17.763 1070 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.47 % Allowed : 16.67 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.26), residues: 1006 helix: 0.59 (0.24), residues: 486 sheet: -0.92 (0.48), residues: 95 loop : -0.50 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 927 HIS 0.003 0.000 HIS A 405 PHE 0.025 0.001 PHE A 759 TYR 0.009 0.001 TYR A 836 ARG 0.003 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 109 time to evaluate : 0.912 Fit side-chains revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7327 (tptp) REVERT: A 157 ASP cc_start: 0.7348 (OUTLIER) cc_final: 0.6575 (m-30) REVERT: A 207 MET cc_start: 0.8438 (mmm) cc_final: 0.7938 (mmm) REVERT: A 218 LYS cc_start: 0.8161 (ttmt) cc_final: 0.7930 (ttmt) REVERT: A 238 GLU cc_start: 0.7149 (tt0) cc_final: 0.6745 (tt0) REVERT: A 259 GLN cc_start: 0.5954 (mt0) cc_final: 0.5597 (mt0) REVERT: A 380 ASN cc_start: 0.7864 (OUTLIER) cc_final: 0.7642 (m110) REVERT: A 384 ILE cc_start: 0.8205 (mm) cc_final: 0.7910 (mm) REVERT: A 413 LEU cc_start: 0.8056 (tp) cc_final: 0.7573 (tt) REVERT: A 439 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6911 (tm-30) REVERT: A 452 MET cc_start: 0.8484 (ptt) cc_final: 0.8154 (ptt) REVERT: A 466 GLU cc_start: 0.7375 (pm20) cc_final: 0.6472 (tp30) REVERT: A 487 PHE cc_start: 0.6606 (t80) cc_final: 0.6166 (t80) REVERT: A 508 MET cc_start: 0.4863 (OUTLIER) cc_final: 0.3251 (tpp) REVERT: A 559 ARG cc_start: 0.7795 (mtp85) cc_final: 0.7435 (mtm110) REVERT: A 575 MET cc_start: 0.3129 (mmp) cc_final: 0.2805 (mmt) REVERT: A 699 MET cc_start: 0.8070 (tpt) cc_final: 0.5717 (tpt) REVERT: A 731 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6327 (mp0) REVERT: A 824 LYS cc_start: 0.7276 (mmtt) cc_final: 0.6681 (mmpt) REVERT: A 917 GLU cc_start: 0.7627 (tp30) cc_final: 0.7289 (tp30) REVERT: A 923 ARG cc_start: 0.5268 (mmt-90) cc_final: 0.4826 (mmt90) REVERT: A 1023 MET cc_start: 0.3371 (tmt) cc_final: 0.2469 (ptt) outliers start: 30 outliers final: 12 residues processed: 129 average time/residue: 1.1818 time to fit residues: 161.8562 Evaluate side-chains 122 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 104 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 595 CYS Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 669 CYS Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 916 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 918 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7968 Z= 0.246 Angle : 0.538 6.225 10813 Z= 0.285 Chirality : 0.043 0.199 1269 Planarity : 0.005 0.048 1378 Dihedral : 4.223 20.991 1070 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.70 % Allowed : 17.25 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.26), residues: 1006 helix: 0.35 (0.24), residues: 491 sheet: -0.87 (0.48), residues: 94 loop : -0.55 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 927 HIS 0.003 0.001 HIS A 405 PHE 0.029 0.002 PHE A 759 TYR 0.010 0.001 TYR A 836 ARG 0.002 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 106 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7376 (tptp) REVERT: A 157 ASP cc_start: 0.7565 (OUTLIER) cc_final: 0.6798 (m-30) REVERT: A 207 MET cc_start: 0.8454 (mmm) cc_final: 0.8077 (mmm) REVERT: A 218 LYS cc_start: 0.8204 (ttmt) cc_final: 0.7931 (ttmt) REVERT: A 238 GLU cc_start: 0.7131 (tt0) cc_final: 0.6698 (tt0) REVERT: A 259 GLN cc_start: 0.6198 (mt0) cc_final: 0.5810 (mt0) REVERT: A 380 ASN cc_start: 0.7883 (OUTLIER) cc_final: 0.7642 (m110) REVERT: A 384 ILE cc_start: 0.8285 (mm) cc_final: 0.7876 (mp) REVERT: A 413 LEU cc_start: 0.8110 (tp) cc_final: 0.7619 (tt) REVERT: A 439 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.7045 (tm-30) REVERT: A 466 GLU cc_start: 0.7430 (pm20) cc_final: 0.6550 (tp30) REVERT: A 487 PHE cc_start: 0.6591 (t80) cc_final: 0.6184 (t80) REVERT: A 559 ARG cc_start: 0.7830 (mtp85) cc_final: 0.7454 (mtm110) REVERT: A 575 MET cc_start: 0.3077 (mmp) cc_final: 0.2674 (mmt) REVERT: A 699 MET cc_start: 0.8089 (tpt) cc_final: 0.5694 (tpt) REVERT: A 702 ASP cc_start: 0.7775 (OUTLIER) cc_final: 0.6917 (p0) REVERT: A 731 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.6229 (mp0) REVERT: A 756 MET cc_start: 0.7176 (OUTLIER) cc_final: 0.6908 (mtp) REVERT: A 824 LYS cc_start: 0.7309 (mmtt) cc_final: 0.6716 (mmpt) REVERT: A 855 PHE cc_start: 0.7205 (OUTLIER) cc_final: 0.6993 (m-10) REVERT: A 917 GLU cc_start: 0.7815 (tp30) cc_final: 0.7338 (tp30) REVERT: A 923 ARG cc_start: 0.5214 (mmt-90) cc_final: 0.4801 (mmt90) REVERT: A 1023 MET cc_start: 0.3454 (tmt) cc_final: 0.2529 (ptt) outliers start: 32 outliers final: 19 residues processed: 128 average time/residue: 1.1458 time to fit residues: 156.2581 Evaluate side-chains 130 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 103 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 595 CYS Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 669 CYS Chi-restraints excluded: chain A residue 702 ASP Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 916 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 85 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 918 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7968 Z= 0.164 Angle : 0.494 6.914 10813 Z= 0.262 Chirality : 0.041 0.167 1269 Planarity : 0.005 0.047 1378 Dihedral : 4.060 18.271 1070 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.47 % Allowed : 17.59 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.26), residues: 1006 helix: 0.49 (0.24), residues: 492 sheet: -0.81 (0.48), residues: 94 loop : -0.51 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 927 HIS 0.004 0.001 HIS A 405 PHE 0.025 0.001 PHE A 759 TYR 0.009 0.001 TYR A 836 ARG 0.003 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 107 time to evaluate : 0.730 Fit side-chains revert: symmetry clash REVERT: A 33 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7310 (tptp) REVERT: A 157 ASP cc_start: 0.7378 (OUTLIER) cc_final: 0.6609 (m-30) REVERT: A 207 MET cc_start: 0.8445 (mmm) cc_final: 0.7920 (mmm) REVERT: A 218 LYS cc_start: 0.8171 (ttmt) cc_final: 0.7925 (ttmt) REVERT: A 238 GLU cc_start: 0.7120 (tt0) cc_final: 0.6691 (tt0) REVERT: A 259 GLN cc_start: 0.6158 (mt0) cc_final: 0.5772 (mt0) REVERT: A 380 ASN cc_start: 0.7845 (OUTLIER) cc_final: 0.7622 (m110) REVERT: A 384 ILE cc_start: 0.8207 (mm) cc_final: 0.7763 (mp) REVERT: A 413 LEU cc_start: 0.8076 (tp) cc_final: 0.7598 (tt) REVERT: A 466 GLU cc_start: 0.7368 (pm20) cc_final: 0.6527 (tp30) REVERT: A 487 PHE cc_start: 0.6585 (t80) cc_final: 0.6169 (t80) REVERT: A 494 MET cc_start: 0.7043 (ppp) cc_final: 0.6789 (ppp) REVERT: A 559 ARG cc_start: 0.7807 (mtp85) cc_final: 0.7444 (mtm110) REVERT: A 575 MET cc_start: 0.3371 (mmp) cc_final: 0.3014 (mmt) REVERT: A 699 MET cc_start: 0.8069 (tpt) cc_final: 0.5756 (tpt) REVERT: A 702 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.7231 (p0) REVERT: A 731 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6333 (mp0) REVERT: A 756 MET cc_start: 0.7162 (OUTLIER) cc_final: 0.6836 (mtp) REVERT: A 824 LYS cc_start: 0.7291 (mmtt) cc_final: 0.6700 (mmpt) REVERT: A 917 GLU cc_start: 0.7657 (tp30) cc_final: 0.7260 (tp30) REVERT: A 923 ARG cc_start: 0.5204 (mmt-90) cc_final: 0.4783 (mmt90) REVERT: A 1023 MET cc_start: 0.3736 (tmt) cc_final: 0.2865 (ptt) outliers start: 30 outliers final: 21 residues processed: 127 average time/residue: 1.1704 time to fit residues: 158.1648 Evaluate side-chains 130 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 103 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 595 CYS Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 669 CYS Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 702 ASP Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 949 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 71 optimal weight: 0.0870 chunk 27 optimal weight: 0.4980 chunk 81 optimal weight: 0.0000 chunk 85 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 ASN A 918 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7968 Z= 0.143 Angle : 0.485 6.890 10813 Z= 0.257 Chirality : 0.041 0.187 1269 Planarity : 0.005 0.046 1378 Dihedral : 3.915 17.198 1070 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.89 % Allowed : 18.52 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.26), residues: 1006 helix: 0.59 (0.24), residues: 492 sheet: -0.69 (0.50), residues: 92 loop : -0.44 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 927 HIS 0.003 0.000 HIS A 405 PHE 0.025 0.001 PHE A 759 TYR 0.009 0.001 TYR A 836 ARG 0.003 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 102 time to evaluate : 0.856 Fit side-chains revert: symmetry clash REVERT: A 33 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7230 (tptp) REVERT: A 157 ASP cc_start: 0.7342 (OUTLIER) cc_final: 0.6590 (m-30) REVERT: A 207 MET cc_start: 0.8432 (mmm) cc_final: 0.7924 (mmm) REVERT: A 218 LYS cc_start: 0.8156 (ttmt) cc_final: 0.7911 (ttmt) REVERT: A 238 GLU cc_start: 0.7063 (tt0) cc_final: 0.6648 (tt0) REVERT: A 259 GLN cc_start: 0.6126 (mt0) cc_final: 0.5802 (mt0) REVERT: A 413 LEU cc_start: 0.8046 (tp) cc_final: 0.7594 (tt) REVERT: A 466 GLU cc_start: 0.7345 (pm20) cc_final: 0.6512 (tp30) REVERT: A 487 PHE cc_start: 0.6582 (t80) cc_final: 0.6173 (t80) REVERT: A 494 MET cc_start: 0.7065 (ppp) cc_final: 0.6779 (ppp) REVERT: A 559 ARG cc_start: 0.7801 (mtp85) cc_final: 0.7411 (mtm110) REVERT: A 575 MET cc_start: 0.3126 (mmp) cc_final: 0.2799 (mmt) REVERT: A 699 MET cc_start: 0.8080 (tpt) cc_final: 0.5720 (tpt) REVERT: A 702 ASP cc_start: 0.7439 (OUTLIER) cc_final: 0.7075 (p0) REVERT: A 731 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6593 (mp0) REVERT: A 756 MET cc_start: 0.7172 (OUTLIER) cc_final: 0.6837 (mtp) REVERT: A 824 LYS cc_start: 0.7284 (mmtt) cc_final: 0.6693 (mmpt) REVERT: A 917 GLU cc_start: 0.7650 (tp30) cc_final: 0.7120 (tp30) REVERT: A 923 ARG cc_start: 0.5226 (mmt-90) cc_final: 0.4799 (mmt90) REVERT: A 1023 MET cc_start: 0.3652 (tmt) cc_final: 0.2795 (ptt) outliers start: 25 outliers final: 16 residues processed: 122 average time/residue: 1.1769 time to fit residues: 152.4595 Evaluate side-chains 121 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 100 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 595 CYS Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 669 CYS Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 702 ASP Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 949 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 chunk 92 optimal weight: 0.9990 chunk 80 optimal weight: 0.3980 chunk 8 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 ASN A 918 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7968 Z= 0.165 Angle : 0.496 6.736 10813 Z= 0.261 Chirality : 0.041 0.168 1269 Planarity : 0.005 0.045 1378 Dihedral : 3.926 18.148 1070 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.55 % Allowed : 19.10 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.26), residues: 1006 helix: 0.66 (0.24), residues: 488 sheet: -0.73 (0.49), residues: 92 loop : -0.46 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 927 HIS 0.003 0.001 HIS A 405 PHE 0.026 0.001 PHE A 759 TYR 0.009 0.001 TYR A 836 ARG 0.002 0.000 ARG A 246 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 98 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: A 33 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7247 (tptp) REVERT: A 157 ASP cc_start: 0.7308 (OUTLIER) cc_final: 0.6558 (m-30) REVERT: A 207 MET cc_start: 0.8367 (mmm) cc_final: 0.7843 (mmm) REVERT: A 218 LYS cc_start: 0.8172 (ttmt) cc_final: 0.7920 (ttmt) REVERT: A 238 GLU cc_start: 0.7063 (tt0) cc_final: 0.6645 (tt0) REVERT: A 259 GLN cc_start: 0.6155 (mt0) cc_final: 0.5755 (mt0) REVERT: A 413 LEU cc_start: 0.8032 (tp) cc_final: 0.7586 (tt) REVERT: A 466 GLU cc_start: 0.7363 (pm20) cc_final: 0.6519 (tp30) REVERT: A 487 PHE cc_start: 0.6576 (t80) cc_final: 0.6175 (t80) REVERT: A 494 MET cc_start: 0.7074 (ppp) cc_final: 0.6763 (ppp) REVERT: A 508 MET cc_start: 0.4831 (tmm) cc_final: 0.3252 (tpp) REVERT: A 559 ARG cc_start: 0.7816 (mtp85) cc_final: 0.7398 (mtm110) REVERT: A 575 MET cc_start: 0.3208 (mmp) cc_final: 0.2883 (mmt) REVERT: A 699 MET cc_start: 0.8099 (tpt) cc_final: 0.5794 (tpt) REVERT: A 702 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.7040 (p0) REVERT: A 731 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6619 (mp0) REVERT: A 756 MET cc_start: 0.7196 (OUTLIER) cc_final: 0.6853 (mtp) REVERT: A 824 LYS cc_start: 0.7295 (mmtt) cc_final: 0.6700 (mmpt) REVERT: A 917 GLU cc_start: 0.7663 (tp30) cc_final: 0.7134 (tp30) REVERT: A 1023 MET cc_start: 0.3519 (tmt) cc_final: 0.2701 (ptt) outliers start: 22 outliers final: 17 residues processed: 114 average time/residue: 1.1958 time to fit residues: 144.8748 Evaluate side-chains 120 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 98 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 595 CYS Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 669 CYS Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 702 ASP Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 949 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 80 optimal weight: 0.4980 chunk 33 optimal weight: 0.3980 chunk 82 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 ASN A 918 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.204198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.161051 restraints weight = 8192.211| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 1.69 r_work: 0.3599 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7968 Z= 0.160 Angle : 0.490 6.716 10813 Z= 0.257 Chirality : 0.041 0.167 1269 Planarity : 0.005 0.046 1378 Dihedral : 3.887 18.218 1070 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.66 % Allowed : 18.98 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.26), residues: 1006 helix: 0.69 (0.24), residues: 488 sheet: -0.69 (0.50), residues: 92 loop : -0.46 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 927 HIS 0.002 0.000 HIS A 405 PHE 0.026 0.001 PHE A 759 TYR 0.009 0.001 TYR A 836 ARG 0.002 0.000 ARG A 246 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3234.68 seconds wall clock time: 58 minutes 3.39 seconds (3483.39 seconds total)