Starting phenix.real_space_refine on Fri Sep 11 07:59:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xmq_22261/09_2026/6xmq_22261.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xmq_22261/09_2026/6xmq_22261.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xmq_22261/09_2026/6xmq_22261.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xmq_22261/09_2026/6xmq_22261.map" model { file = "/net/cci-nas-00/data/ceres_data/6xmq_22261/09_2026/6xmq_22261.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xmq_22261/09_2026/6xmq_22261.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6xmq_22261/09_2026/6xmq_22261.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xmq_22261/09_2026/6xmq_22261.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= -0.001 sd= 0.055 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 37 5.16 5 C 5410 2.51 5 N 1375 2.21 5 O 1536 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8362 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1085, 8330 Classifications: {'peptide': 1085} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 48, 'TRANS': 1036} Chain breaks: 3 Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 241 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 3, 'GLU:plan': 13, 'TYR:plan': 2, 'ASP:plan': 8, 'ARG:plan': 5, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 142 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ACP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.51, per 1000 atoms: 0.18 Number of scatterers: 8362 At special positions: 0 Unit cell: (84.49, 95.2, 136.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 37 16.00 P 3 15.00 Mg 1 11.99 O 1536 8.00 N 1375 7.00 C 5410 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 - 3.00 Amino acid : True - 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: 0.76 Conformation dependent library (CDL) restraints added in 254.4 milliseconds 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2042 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 9 sheets defined 48.2% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 28 through 44 removed outlier: 3.595A pdb=" N PHE A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Proline residue: A 34 - end of helix Processing helix chain 'A' and resid 57 through 74 removed outlier: 3.701A pdb=" N LEU A 61 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 77 No H-bonds generated for 'chain 'A' and resid 75 through 77' Processing helix chain 'A' and resid 78 through 86 Processing helix chain 'A' and resid 149 through 154 removed outlier: 3.830A pdb=" N GLU A 153 " --> pdb=" O PHE A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 163 removed outlier: 3.956A pdb=" N GLN A 161 " --> pdb=" O ILE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 Processing helix chain 'A' and resid 188 through 198 removed outlier: 3.880A pdb=" N VAL A 198 " --> pdb=" O LYS A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 215 Processing helix chain 'A' and resid 218 through 247 removed outlier: 3.524A pdb=" N ARG A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 250 No H-bonds generated for 'chain 'A' and resid 248 through 250' Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 372 through 375 removed outlier: 3.791A pdb=" N GLU A 375 " --> pdb=" O THR A 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 372 through 375' Processing helix chain 'A' and resid 376 through 387 Processing helix chain 'A' and resid 396 through 424 removed outlier: 3.813A pdb=" N LEU A 400 " --> pdb=" O ASN A 396 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR A 416 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 443 removed outlier: 4.536A pdb=" N LEU A 433 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP A 434 " --> pdb=" O LYS A 430 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL A 443 " --> pdb=" O ILE A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 463 removed outlier: 4.096A pdb=" N MET A 453 " --> pdb=" O MET A 449 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 473 No H-bonds generated for 'chain 'A' and resid 471 through 473' Processing helix chain 'A' and resid 474 through 480 removed outlier: 4.258A pdb=" N ARG A 480 " --> pdb=" O PRO A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 532 removed outlier: 3.717A pdb=" N ILE A 526 " --> pdb=" O PRO A 522 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY A 530 " --> pdb=" O ILE A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 557 Processing helix chain 'A' and resid 606 through 611 Processing helix chain 'A' and resid 620 through 630 removed outlier: 3.848A pdb=" N TYR A 625 " --> pdb=" O TYR A 621 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS A 626 " --> pdb=" O ASP A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 689 removed outlier: 3.659A pdb=" N THR A 682 " --> pdb=" O ASP A 678 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE A 683 " --> pdb=" O ALA A 679 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS A 684 " --> pdb=" O ILE A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 712 removed outlier: 3.512A pdb=" N ALA A 704 " --> pdb=" O ASN A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 758 Processing helix chain 'A' and resid 767 through 773 Processing helix chain 'A' and resid 778 through 786 removed outlier: 3.697A pdb=" N ARG A 784 " --> pdb=" O ARG A 780 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N HIS A 785 " --> pdb=" O ASP A 781 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR A 786 " --> pdb=" O LEU A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 808 removed outlier: 3.743A pdb=" N GLY A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 819 No H-bonds generated for 'chain 'A' and resid 817 through 819' Processing helix chain 'A' and resid 820 through 827 Processing helix chain 'A' and resid 837 through 851 Processing helix chain 'A' and resid 972 through 1012 removed outlier: 4.370A pdb=" N ALA A1012 " --> pdb=" O ILE A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1036 removed outlier: 4.107A pdb=" N CYS A1031 " --> pdb=" O LEU A1027 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N SER A1036 " --> pdb=" O PHE A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1084 Processing helix chain 'A' and resid 1099 through 1121 removed outlier: 4.139A pdb=" N PHE A1117 " --> pdb=" O GLN A1113 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A1118 " --> pdb=" O VAL A1114 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1152 removed outlier: 3.889A pdb=" N TYR A1137 " --> pdb=" O ASN A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1162 removed outlier: 3.996A pdb=" N ASN A1159 " --> pdb=" O LEU A1155 " (cutoff:3.500A) Processing helix chain 'A' and resid 1168 through 1198 removed outlier: 4.114A pdb=" N ILE A1173 " --> pdb=" O ASP A1169 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS A1174 " --> pdb=" O ASP A1170 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A1179 " --> pdb=" O LEU A1175 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET A1198 " --> pdb=" O LYS A1194 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 8 removed outlier: 3.640A pdb=" N VAL A 143 " --> pdb=" O HIS A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.801A pdb=" N TYR A 102 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N SER A 15 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU A 100 " --> pdb=" O SER A 15 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LEU A 17 " --> pdb=" O HIS A 98 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N HIS A 98 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY A 111 " --> pdb=" O ILE A 101 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 116 through 120 Processing sheet with id=AA4, first strand: chain 'A' and resid 129 through 130 removed outlier: 3.565A pdb=" N PHE A 130 " --> pdb=" O LYS A 133 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 263 through 267 removed outlier: 4.715A pdb=" N ASN A 257 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER A 279 " --> pdb=" O ASN A 257 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU A 277 " --> pdb=" O PHE A 259 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU A 366 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU A 296 " --> pdb=" O LEU A 366 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ASP A 292 " --> pdb=" O THR A 370 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 316 through 317 removed outlier: 6.682A pdb=" N SER A 299 " --> pdb=" O VAL A 348 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL A 348 " --> pdb=" O SER A 299 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE A 301 " --> pdb=" O LEU A 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 467 through 469 removed outlier: 6.729A pdb=" N GLY A 830 " --> pdb=" O PHE A 964 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N SER A 966 " --> pdb=" O GLY A 830 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ALA A 832 " --> pdb=" O SER A 966 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A 829 " --> pdb=" O THR A 811 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP A 487 " --> pdb=" O CYS A 814 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N CYS A 484 " --> pdb=" O ILE A 694 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ILE A 696 " --> pdb=" O CYS A 484 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N PHE A 486 " --> pdb=" O ILE A 696 " (cutoff:3.500A) removed outlier: 9.075A pdb=" N TYR A 789 " --> pdb=" O SER A 693 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N MET A 695 " --> pdb=" O TYR A 789 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LEU A 719 " --> pdb=" O ALA A 764 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N THR A 766 " --> pdb=" O LEU A 719 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU A 721 " --> pdb=" O THR A 766 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 515 through 516 removed outlier: 3.642A pdb=" N VAL A 498 " --> pdb=" O HIS A 672 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ILE A 670 " --> pdb=" O GLU A 500 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LEU A 502 " --> pdb=" O PHE A 668 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N PHE A 668 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N PHE A 665 " --> pdb=" O SER A 640 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N SER A 640 " --> pdb=" O PHE A 665 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY A 667 " --> pdb=" O LEU A 638 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE A 600 " --> pdb=" O ALA A 593 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG A 578 " --> pdb=" O ILE A 592 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N SER A 594 " --> pdb=" O ILE A 576 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ILE A 576 " --> pdb=" O SER A 594 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 536 through 537 removed outlier: 3.880A pdb=" N VAL A 536 " --> pdb=" O VAL A 544 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A 544 " --> pdb=" O VAL A 536 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 403 hydrogen bonds defined for protein. 1182 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: 1.44 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2661 1.35 - 1.48: 2089 1.48 - 1.60: 3725 1.60 - 1.73: 4 1.73 - 1.86: 64 Bond restraints: 8543 Sorted by residual: bond pdb=" C1' ACP A1301 " pdb=" O4' ACP A1301 " ideal model delta sigma weight residual 1.390 1.615 -0.225 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C1' ACP A1301 " pdb=" C2' ACP A1301 " ideal model delta sigma weight residual 1.527 1.304 0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" C4' ACP A1301 " pdb=" O4' ACP A1301 " ideal model delta sigma weight residual 1.428 1.301 0.127 2.00e-02 2.50e+03 4.04e+01 bond pdb=" C6 ACP A1301 " pdb=" N6 ACP A1301 " ideal model delta sigma weight residual 1.335 1.448 -0.113 2.00e-02 2.50e+03 3.21e+01 bond pdb=" C2' ACP A1301 " pdb=" O2' ACP A1301 " ideal model delta sigma weight residual 1.401 1.490 -0.089 2.00e-02 2.50e+03 1.99e+01 ... (remaining 8538 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 11500 2.65 - 5.30: 99 5.30 - 7.95: 3 7.95 - 10.60: 7 10.60 - 13.25: 1 Bond angle restraints: 11610 Sorted by residual: angle pdb=" O3A ACP A1301 " pdb=" PA ACP A1301 " pdb=" O5' ACP A1301 " ideal model delta sigma weight residual 93.75 107.00 -13.25 3.00e+00 1.11e-01 1.95e+01 angle pdb=" N1 ACP A1301 " pdb=" C6 ACP A1301 " pdb=" N6 ACP A1301 " ideal model delta sigma weight residual 119.32 108.84 10.48 3.00e+00 1.11e-01 1.22e+01 angle pdb=" C3B ACP A1301 " pdb=" PB ACP A1301 " pdb=" O3A ACP A1301 " ideal model delta sigma weight residual 98.05 108.34 -10.29 3.00e+00 1.11e-01 1.18e+01 angle pdb=" O1B ACP A1301 " pdb=" PB ACP A1301 " pdb=" O2B ACP A1301 " ideal model delta sigma weight residual 119.60 110.06 9.54 3.00e+00 1.11e-01 1.01e+01 angle pdb=" O1A ACP A1301 " pdb=" PA ACP A1301 " pdb=" O2A ACP A1301 " ideal model delta sigma weight residual 118.95 110.47 8.48 3.00e+00 1.11e-01 7.99e+00 ... (remaining 11605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.49: 4734 18.49 - 36.98: 310 36.98 - 55.46: 31 55.46 - 73.95: 5 73.95 - 92.44: 8 Dihedral angle restraints: 5088 sinusoidal: 1936 harmonic: 3152 Sorted by residual: dihedral pdb=" O1B ACP A1301 " pdb=" C3B ACP A1301 " pdb=" PB ACP A1301 " pdb=" PG ACP A1301 " ideal model delta sinusoidal sigma weight residual -52.82 39.62 -92.44 1 3.00e+01 1.11e-03 1.11e+01 dihedral pdb=" CB GLU A 420 " pdb=" CG GLU A 420 " pdb=" CD GLU A 420 " pdb=" OE1 GLU A 420 " ideal model delta sinusoidal sigma weight residual 0.00 89.81 -89.81 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU A 520 " pdb=" CG GLU A 520 " pdb=" CD GLU A 520 " pdb=" OE1 GLU A 520 " ideal model delta sinusoidal sigma weight residual 0.00 89.40 -89.40 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 5085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1163 0.057 - 0.114: 180 0.114 - 0.171: 18 0.171 - 0.227: 0 0.227 - 0.284: 1 Chirality restraints: 1362 Sorted by residual: chirality pdb=" C2' ACP A1301 " pdb=" C1' ACP A1301 " pdb=" C3' ACP A1301 " pdb=" O2' ACP A1301 " both_signs ideal model delta sigma weight residual False -2.75 -2.47 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA ILE A 301 " pdb=" N ILE A 301 " pdb=" C ILE A 301 " pdb=" CB ILE A 301 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA ILE A 289 " pdb=" N ILE A 289 " pdb=" C ILE A 289 " pdb=" CB ILE A 289 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.49e-01 ... (remaining 1359 not shown) Planarity restraints: 1460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A1039 " 0.023 5.00e-02 4.00e+02 3.55e-02 2.02e+00 pdb=" N PRO A1040 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A1040 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A1040 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 273 " -0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO A 274 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 274 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 274 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 962 " 0.020 5.00e-02 4.00e+02 3.05e-02 1.49e+00 pdb=" N PRO A 963 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 963 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 963 " 0.017 5.00e-02 4.00e+02 ... (remaining 1457 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.31: 18 2.31 - 2.96: 3914 2.96 - 3.60: 11684 3.60 - 4.25: 16694 4.25 - 4.90: 28749 Nonbonded interactions: 61059 Sorted by model distance: nonbonded pdb=" O3G ACP A1301 " pdb="MG MG A1302 " model vdw 1.660 2.170 nonbonded pdb=" OD2 ASP A 816 " pdb="MG MG A1302 " model vdw 2.005 2.170 nonbonded pdb=" OD2 ASP A 487 " pdb="MG MG A1302 " model vdw 2.042 2.170 nonbonded pdb=" OD2 ASP A 487 " pdb=" O3G ACP A1301 " model vdw 2.080 3.040 nonbonded pdb=" OD1 ASP A 816 " pdb="MG MG A1302 " model vdw 2.102 2.170 ... (remaining 61054 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.500 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.060 Set ADP refinement strategy: 0.020 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 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 : 0.006 0.225 8543 Z= 0.287 Angle : 0.662 13.253 11610 Z= 0.343 Chirality : 0.042 0.284 1362 Planarity : 0.004 0.036 1460 Dihedral : 12.803 92.440 3046 Min Nonbonded Distance : 1.660 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.23), residues: 1077 helix: -0.19 (0.21), residues: 489 sheet: -1.75 (0.40), residues: 132 loop : -1.80 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 613 TYR 0.013 0.001 TYR A 625 PHE 0.016 0.002 PHE A 237 TRP 0.006 0.001 TRP A 137 HIS 0.004 0.001 HIS A 706 Details of bonding type rmsd/Z covalent geometry : bond 0.00614 / 0.29 ( 8543) covalent geometry : angle 0.66219 / 0.34 (11610) hydrogen bonds : bond 0.17257 / 11.05 ( 403) hydrogen bonds : angle 6.23827 / 4.30 ( 1182) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.225 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.0816 time to fit residues: 7.9984 Evaluate side-chains 36 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.0010 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 129 GLN A 166 HIS A 514 HIS ** A 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 776 HIS A 785 HIS A 826 GLN A 987 ASN A1065 GLN A1069 HIS A1122 GLN A1209 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.072634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.061011 restraints weight = 31048.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.062891 restraints weight = 16577.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.064164 restraints weight = 11052.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.064979 restraints weight = 8374.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.065558 restraints weight = 6940.404| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8543 Z= 0.121 Angle : 0.524 8.297 11610 Z= 0.273 Chirality : 0.039 0.146 1362 Planarity : 0.004 0.032 1460 Dihedral : 4.982 67.089 1150 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.24 % Allowed : 9.11 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.25), residues: 1077 helix: 1.37 (0.23), residues: 490 sheet: -1.56 (0.39), residues: 149 loop : -1.24 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 239 TYR 0.010 0.001 TYR A 28 PHE 0.015 0.001 PHE A1016 TRP 0.006 0.001 TRP A 212 HIS 0.005 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 8543) covalent geometry : angle 0.52415 / 0.27 (11610) hydrogen bonds : bond 0.05313 / 3.47 ( 403) hydrogen bonds : angle 4.34310 / 2.99 ( 1182) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.330 Fit side-chains REVERT: A 239 ARG cc_start: 0.9019 (mmm-85) cc_final: 0.8796 (tpt170) REVERT: A 246 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.8035 (t80) outliers start: 11 outliers final: 4 residues processed: 52 average time/residue: 0.0789 time to fit residues: 6.4276 Evaluate side-chains 40 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1146 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 11 optimal weight: 6.9990 chunk 12 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 82 optimal weight: 20.0000 chunk 106 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 63 optimal weight: 0.0030 chunk 68 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 overall best weight: 2.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.069552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.057643 restraints weight = 31276.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.059520 restraints weight = 16607.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.060780 restraints weight = 11040.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.061586 restraints weight = 8390.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.062089 restraints weight = 6991.111| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8543 Z= 0.182 Angle : 0.554 6.796 11610 Z= 0.286 Chirality : 0.040 0.142 1362 Planarity : 0.004 0.031 1460 Dihedral : 4.847 59.382 1150 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.46 % Allowed : 12.71 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.26), residues: 1077 helix: 1.85 (0.24), residues: 485 sheet: -1.27 (0.42), residues: 141 loop : -1.03 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 634 TYR 0.012 0.001 TYR A 625 PHE 0.013 0.001 PHE A 499 TRP 0.006 0.001 TRP A 137 HIS 0.004 0.001 HIS A 706 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 ( 8543) covalent geometry : angle 0.55372 / 0.29 (11610) hydrogen bonds : bond 0.05512 / 3.61 ( 403) hydrogen bonds : angle 4.16579 / 2.85 ( 1182) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.347 Fit side-chains REVERT: A 239 ARG cc_start: 0.9116 (mmm-85) cc_final: 0.8856 (tpt170) REVERT: A 807 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8497 (mtm) REVERT: A 1162 MET cc_start: 0.9086 (mmm) cc_final: 0.8799 (tpt) REVERT: A 1198 MET cc_start: 0.8367 (tpt) cc_final: 0.8165 (tpp) outliers start: 13 outliers final: 9 residues processed: 45 average time/residue: 0.0701 time to fit residues: 5.0287 Evaluate side-chains 46 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 762 ASP Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1011 MET Chi-restraints excluded: chain A residue 1146 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 6 optimal weight: 0.0870 chunk 42 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 26 optimal weight: 0.4980 chunk 79 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1065 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.070925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.059278 restraints weight = 31628.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.061153 restraints weight = 16876.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.062398 restraints weight = 11236.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.063261 restraints weight = 8544.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.063782 restraints weight = 7039.493| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8543 Z= 0.150 Angle : 0.510 6.179 11610 Z= 0.265 Chirality : 0.039 0.144 1362 Planarity : 0.003 0.032 1460 Dihedral : 4.560 51.093 1150 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.02 % Allowed : 15.30 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.26), residues: 1077 helix: 2.08 (0.24), residues: 484 sheet: -1.11 (0.42), residues: 141 loop : -0.92 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 634 TYR 0.011 0.001 TYR A 625 PHE 0.012 0.001 PHE A 499 TRP 0.007 0.001 TRP A 137 HIS 0.004 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 8543) covalent geometry : angle 0.51039 / 0.26 (11610) hydrogen bonds : bond 0.05085 / 3.31 ( 403) hydrogen bonds : angle 3.95959 / 2.70 ( 1182) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 37 time to evaluate : 0.199 Fit side-chains REVERT: A 1162 MET cc_start: 0.9082 (mmm) cc_final: 0.8656 (tpt) outliers start: 18 outliers final: 11 residues processed: 50 average time/residue: 0.0557 time to fit residues: 4.5006 Evaluate side-chains 48 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 762 ASP Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1011 MET Chi-restraints excluded: chain A residue 1035 ILE Chi-restraints excluded: chain A residue 1092 LEU Chi-restraints excluded: chain A residue 1146 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 44 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 129 GLN A 327 ASN ** A 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.069449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.057791 restraints weight = 31587.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.059606 restraints weight = 16948.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.060853 restraints weight = 11378.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.061607 restraints weight = 8658.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.062254 restraints weight = 7239.026| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 8543 Z= 0.213 Angle : 0.577 8.009 11610 Z= 0.297 Chirality : 0.040 0.143 1362 Planarity : 0.004 0.031 1460 Dihedral : 4.590 40.925 1150 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.47 % Allowed : 16.76 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.26), residues: 1077 helix: 2.06 (0.24), residues: 484 sheet: -1.04 (0.44), residues: 142 loop : -0.92 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 634 TYR 0.014 0.001 TYR A 625 PHE 0.016 0.001 PHE A 499 TRP 0.006 0.001 TRP A 137 HIS 0.004 0.001 HIS A 706 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.21 ( 8543) covalent geometry : angle 0.57669 / 0.30 (11610) hydrogen bonds : bond 0.05674 / 3.70 ( 403) hydrogen bonds : angle 4.15341 / 2.83 ( 1182) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 36 time to evaluate : 0.379 Fit side-chains REVERT: A 246 PHE cc_start: 0.8553 (OUTLIER) cc_final: 0.8263 (t80) REVERT: A 295 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8448 (mm) REVERT: A 807 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8515 (mtm) outliers start: 22 outliers final: 16 residues processed: 51 average time/residue: 0.0634 time to fit residues: 5.3938 Evaluate side-chains 55 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 36 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 762 ASP Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1011 MET Chi-restraints excluded: chain A residue 1035 ILE Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1092 LEU Chi-restraints excluded: chain A residue 1146 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 81 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 2 optimal weight: 0.4980 chunk 63 optimal weight: 0.0980 chunk 26 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 129 GLN ** A 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.070302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.058360 restraints weight = 31280.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.060269 restraints weight = 16583.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.061554 restraints weight = 11028.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.062354 restraints weight = 8360.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.062988 restraints weight = 6960.901| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8543 Z= 0.123 Angle : 0.491 6.592 11610 Z= 0.253 Chirality : 0.038 0.142 1362 Planarity : 0.003 0.033 1460 Dihedral : 4.225 32.620 1150 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.14 % Allowed : 18.45 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.26), residues: 1077 helix: 2.38 (0.24), residues: 478 sheet: -0.96 (0.43), residues: 141 loop : -0.90 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 634 TYR 0.010 0.001 TYR A 625 PHE 0.010 0.001 PHE A 405 TRP 0.007 0.001 TRP A 137 HIS 0.004 0.001 HIS A 706 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 8543) covalent geometry : angle 0.49098 / 0.25 (11610) hydrogen bonds : bond 0.04682 / 3.03 ( 403) hydrogen bonds : angle 3.78692 / 2.58 ( 1182) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 39 time to evaluate : 0.304 Fit side-chains REVERT: A 246 PHE cc_start: 0.8531 (OUTLIER) cc_final: 0.8288 (t80) outliers start: 19 outliers final: 12 residues processed: 51 average time/residue: 0.0639 time to fit residues: 5.4726 Evaluate side-chains 50 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 762 ASP Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1146 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 2 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 chunk 88 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 chunk 68 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.070136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.058256 restraints weight = 31417.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.060157 restraints weight = 16597.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.061438 restraints weight = 11030.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.062255 restraints weight = 8357.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.062907 restraints weight = 6930.491| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8543 Z= 0.131 Angle : 0.512 10.425 11610 Z= 0.259 Chirality : 0.038 0.142 1362 Planarity : 0.003 0.031 1460 Dihedral : 4.128 27.489 1150 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.14 % Allowed : 18.67 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.26), residues: 1077 helix: 2.42 (0.24), residues: 478 sheet: -0.78 (0.43), residues: 141 loop : -0.88 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 260 TYR 0.010 0.001 TYR A 625 PHE 0.011 0.001 PHE A 499 TRP 0.006 0.001 TRP A 787 HIS 0.003 0.001 HIS A 706 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 8543) covalent geometry : angle 0.51217 / 0.26 (11610) hydrogen bonds : bond 0.04677 / 3.04 ( 403) hydrogen bonds : angle 3.75125 / 2.55 ( 1182) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 37 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 246 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.8294 (t80) outliers start: 19 outliers final: 16 residues processed: 51 average time/residue: 0.0564 time to fit residues: 4.9746 Evaluate side-chains 54 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 37 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 762 ASP Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1035 ILE Chi-restraints excluded: chain A residue 1146 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 89 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 3 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 49 optimal weight: 0.0070 chunk 106 optimal weight: 3.9990 overall best weight: 1.5604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.070172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.058325 restraints weight = 31345.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.060224 restraints weight = 16565.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.061503 restraints weight = 10998.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.062319 restraints weight = 8340.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.062932 restraints weight = 6910.950| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8543 Z= 0.130 Angle : 0.502 8.258 11610 Z= 0.256 Chirality : 0.038 0.142 1362 Planarity : 0.003 0.031 1460 Dihedral : 4.066 24.368 1150 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.14 % Allowed : 19.57 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.26), residues: 1077 helix: 2.47 (0.24), residues: 478 sheet: -0.74 (0.43), residues: 144 loop : -0.84 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 260 TYR 0.010 0.001 TYR A 625 PHE 0.011 0.001 PHE A 499 TRP 0.006 0.001 TRP A 787 HIS 0.003 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 8543) covalent geometry : angle 0.50245 / 0.26 (11610) hydrogen bonds : bond 0.04594 / 2.98 ( 403) hydrogen bonds : angle 3.71364 / 2.53 ( 1182) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 38 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 246 PHE cc_start: 0.8573 (OUTLIER) cc_final: 0.8308 (t80) outliers start: 19 outliers final: 16 residues processed: 52 average time/residue: 0.0615 time to fit residues: 5.4321 Evaluate side-chains 54 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 37 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 762 ASP Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1035 ILE Chi-restraints excluded: chain A residue 1146 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 50 optimal weight: 7.9990 chunk 96 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 32 optimal weight: 0.0040 chunk 10 optimal weight: 3.9990 overall best weight: 1.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.070908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.059417 restraints weight = 31184.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.061294 restraints weight = 16569.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.062543 restraints weight = 11024.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.063354 restraints weight = 8363.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.063905 restraints weight = 6925.579| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8543 Z= 0.131 Angle : 0.510 10.723 11610 Z= 0.257 Chirality : 0.038 0.141 1362 Planarity : 0.003 0.031 1460 Dihedral : 4.026 22.572 1150 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.14 % Allowed : 19.91 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.26), residues: 1077 helix: 2.48 (0.24), residues: 478 sheet: -0.64 (0.44), residues: 141 loop : -0.81 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 260 TYR 0.010 0.001 TYR A 625 PHE 0.011 0.001 PHE A 499 TRP 0.006 0.001 TRP A 787 HIS 0.003 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 8543) covalent geometry : angle 0.51022 / 0.26 (11610) hydrogen bonds : bond 0.04562 / 2.96 ( 403) hydrogen bonds : angle 3.70372 / 2.52 ( 1182) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 38 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 246 PHE cc_start: 0.8545 (OUTLIER) cc_final: 0.8282 (t80) REVERT: A 1136 MET cc_start: 0.8146 (mmm) cc_final: 0.7878 (mmm) outliers start: 19 outliers final: 16 residues processed: 53 average time/residue: 0.0673 time to fit residues: 5.8787 Evaluate side-chains 55 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 38 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 762 ASP Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1035 ILE Chi-restraints excluded: chain A residue 1146 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 93 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 32 optimal weight: 0.1980 chunk 70 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 22 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.071696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.059871 restraints weight = 31202.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.061801 restraints weight = 16358.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.063105 restraints weight = 10817.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.063999 restraints weight = 8167.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.064537 restraints weight = 6695.373| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 8543 Z= 0.096 Angle : 0.497 12.745 11610 Z= 0.247 Chirality : 0.037 0.139 1362 Planarity : 0.003 0.032 1460 Dihedral : 3.831 19.665 1150 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.46 % Allowed : 20.81 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.27), residues: 1077 helix: 2.58 (0.25), residues: 478 sheet: -0.52 (0.44), residues: 141 loop : -0.76 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 175 TYR 0.010 0.001 TYR A1004 PHE 0.010 0.001 PHE A1016 TRP 0.005 0.001 TRP A 137 HIS 0.004 0.000 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 ( 8543) covalent geometry : angle 0.49733 / 0.25 (11610) hydrogen bonds : bond 0.03901 / 2.52 ( 403) hydrogen bonds : angle 3.50999 / 2.39 ( 1182) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 246 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.8229 (t80) outliers start: 13 outliers final: 10 residues processed: 50 average time/residue: 0.0728 time to fit residues: 5.7609 Evaluate side-chains 50 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 762 ASP Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1035 ILE Chi-restraints excluded: chain A residue 1146 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 96 optimal weight: 0.0980 chunk 40 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 30 optimal weight: 0.4980 chunk 83 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.071503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.059630 restraints weight = 31206.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.061566 restraints weight = 16399.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.062860 restraints weight = 10847.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.063760 restraints weight = 8188.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.064290 restraints weight = 6713.704| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8543 Z= 0.100 Angle : 0.500 12.789 11610 Z= 0.248 Chirality : 0.037 0.140 1362 Planarity : 0.003 0.031 1460 Dihedral : 3.786 19.963 1150 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.46 % Allowed : 20.70 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.27), residues: 1077 helix: 2.57 (0.24), residues: 479 sheet: -0.48 (0.44), residues: 141 loop : -0.75 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 239 TYR 0.011 0.001 TYR A1010 PHE 0.010 0.001 PHE A1016 TRP 0.006 0.001 TRP A 787 HIS 0.004 0.000 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 ( 8543) covalent geometry : angle 0.50023 / 0.25 (11610) hydrogen bonds : bond 0.03902 / 2.52 ( 403) hydrogen bonds : angle 3.50391 / 2.39 ( 1182) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1217.32 seconds wall clock time: 21 minutes 46.09 seconds (1306.09 seconds total)