Starting phenix.real_space_refine on Tue Mar 3 19:44:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xmt_22263/03_2026/6xmt_22263.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xmt_22263/03_2026/6xmt_22263.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6xmt_22263/03_2026/6xmt_22263.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xmt_22263/03_2026/6xmt_22263.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xmt_22263/03_2026/6xmt_22263.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xmt_22263/03_2026/6xmt_22263.map" } resolution = 3.3 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= 0.057 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 38 5.16 5 Be 1 3.05 5 C 5370 2.51 5 N 1374 2.21 5 O 1537 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8324 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1092, 8319 Classifications: {'peptide': 1092} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 49, 'TRANS': 1042} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 260 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 221 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'PHE:plan': 4, 'TYR:plan': 4, 'GLN:plan1': 3, 'GLU:plan': 9, 'TRP:plan': 1, 'ASP:plan': 7, 'ARG:plan': 5, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 164 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 5 Unusual residues: {' MG': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.95, per 1000 atoms: 0.23 Number of scatterers: 8324 At special positions: 0 Unit cell: (91.63, 88.06, 145.18, 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 38 16.00 Mg 1 11.99 F 3 9.00 O 1537 8.00 N 1374 7.00 C 5370 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 - 3.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 322.7 milliseconds 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2052 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 46.5% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 28 through 44 removed outlier: 3.804A pdb=" N PHE A 32 " --> pdb=" O TYR A 28 " (cutoff:3.500A) removed outlier: 3.813A 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: 3.540A pdb=" N LEU A 61 " --> pdb=" O THR A 57 " (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 156 through 162 removed outlier: 3.866A pdb=" N PHE A 160 " --> pdb=" O LYS A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 178 Processing helix chain 'A' and resid 188 through 197 Processing helix chain 'A' and resid 199 through 214 Processing helix chain 'A' and resid 218 through 247 removed outlier: 3.697A pdb=" N MET A 231 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU A 232 " --> pdb=" O ILE A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 336 removed outlier: 4.409A pdb=" N ILE A 336 " --> pdb=" O VAL A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 375 removed outlier: 3.703A 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 388 Processing helix chain 'A' and resid 396 through 425 Processing helix chain 'A' and resid 427 through 441 removed outlier: 3.627A pdb=" N ILE A 439 " --> pdb=" O CYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 463 Processing helix chain 'A' and resid 471 through 480 removed outlier: 3.686A pdb=" N ILE A 475 " --> pdb=" O PRO A 472 " (cutoff:3.500A) Proline residue: A 476 - end of helix removed outlier: 3.507A pdb=" N GLY A 479 " --> pdb=" O PRO A 476 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG A 480 " --> pdb=" O PHE A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 532 removed outlier: 3.791A 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 612 removed outlier: 3.777A pdb=" N GLU A 612 " --> pdb=" O GLU A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 630 Processing helix chain 'A' and resid 655 through 660 removed outlier: 4.318A pdb=" N VAL A 659 " --> pdb=" O ASN A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 688 Processing helix chain 'A' and resid 700 through 712 Processing helix chain 'A' and resid 753 through 758 Processing helix chain 'A' and resid 766 through 772 Processing helix chain 'A' and resid 778 through 784 Processing helix chain 'A' and resid 795 through 808 removed outlier: 3.940A pdb=" N PHE A 799 " --> pdb=" O SER A 795 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 827 Processing helix chain 'A' and resid 837 through 854 Processing helix chain 'A' and resid 972 through 1010 removed outlier: 3.667A pdb=" N CYS A 983 " --> pdb=" O ARG A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1035 Processing helix chain 'A' and resid 1055 through 1084 Processing helix chain 'A' and resid 1099 through 1119 removed outlier: 3.903A pdb=" N THR A1103 " --> pdb=" O SER A1099 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE A1108 " --> pdb=" O GLY A1104 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE A1117 " --> pdb=" O GLN A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1152 removed outlier: 3.742A pdb=" N THR A1152 " --> pdb=" O LEU A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1162 Processing helix chain 'A' and resid 1169 through 1197 Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 88 removed outlier: 6.726A pdb=" N TYR A 102 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N SER A 15 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU A 100 " --> pdb=" O SER A 15 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N LEU A 17 " --> pdb=" O HIS A 98 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N HIS A 98 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A 111 " --> pdb=" O ILE A 101 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA3, first strand: chain 'A' and resid 127 through 130 removed outlier: 3.586A pdb=" N PHE A 128 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 263 through 267 removed outlier: 4.862A pdb=" N ASN A 257 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 279 " --> pdb=" O ASN A 257 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LEU A 277 " --> pdb=" O PHE A 259 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASP A 292 " --> pdb=" O THR A 370 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 314 through 316 removed outlier: 6.850A pdb=" N SER A 299 " --> pdb=" O VAL A 348 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N VAL A 348 " --> pdb=" O SER A 299 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE A 301 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS A 344 " --> pdb=" O ASN A 303 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 467 through 469 removed outlier: 6.480A pdb=" N GLY A 830 " --> pdb=" O PHE A 964 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N SER A 966 " --> pdb=" O GLY A 830 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ALA A 832 " --> pdb=" O SER A 966 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N MET A 813 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LEU A 833 " --> pdb=" O MET A 813 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N GLY A 815 " --> pdb=" O LEU A 833 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N CYS A 814 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N CYS A 485 " --> pdb=" O CYS A 814 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N CYS A 484 " --> pdb=" O ILE A 694 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ILE A 696 " --> pdb=" O CYS A 484 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N PHE A 486 " --> pdb=" O ILE A 696 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N SER A 693 " --> pdb=" O TRP A 787 " (cutoff:3.500A) removed outlier: 9.134A pdb=" N TYR A 789 " --> pdb=" O SER A 693 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N MET A 695 " --> pdb=" O TYR A 789 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ILE A 763 " --> pdb=" O THR A 786 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL A 788 " --> pdb=" O ILE A 763 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU A 719 " --> pdb=" O ALA A 764 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP A 722 " --> pdb=" O LEU A 733 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 498 through 501 removed outlier: 3.662A pdb=" N VAL A 498 " --> pdb=" O HIS A 672 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE A 670 " --> pdb=" O GLU A 500 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE A 671 " --> pdb=" O ARG A 634 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 536 through 537 removed outlier: 3.595A pdb=" N VAL A 536 " --> pdb=" O VAL A 544 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 559 through 560 removed outlier: 3.613A pdb=" N ALA A 559 " --> pdb=" O TYR A 567 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 575 through 579 removed outlier: 6.760A pdb=" N ILE A 592 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY A 667 " --> pdb=" O LEU A 638 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N SER A 640 " --> pdb=" O PHE A 665 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N PHE A 665 " --> pdb=" O SER A 640 " (cutoff:3.500A) 402 hydrogen bonds defined for protein. 1167 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: 1.50 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2200 1.33 - 1.45: 1399 1.45 - 1.57: 4832 1.57 - 1.69: 0 1.69 - 1.81: 63 Bond restraints: 8494 Sorted by residual: bond pdb=" F2 BEF A1301 " pdb="BE BEF A1301 " ideal model delta sigma weight residual 1.476 1.560 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" F3 BEF A1301 " pdb="BE BEF A1301 " ideal model delta sigma weight residual 1.476 1.545 -0.069 2.00e-02 2.50e+03 1.17e+01 bond pdb=" F1 BEF A1301 " pdb="BE BEF A1301 " ideal model delta sigma weight residual 1.476 1.534 -0.058 2.00e-02 2.50e+03 8.32e+00 bond pdb=" N VAL A 29 " pdb=" CA VAL A 29 " ideal model delta sigma weight residual 1.460 1.483 -0.023 1.19e-02 7.06e+03 3.79e+00 bond pdb=" CA VAL A 29 " pdb=" C VAL A 29 " ideal model delta sigma weight residual 1.524 1.548 -0.024 1.23e-02 6.61e+03 3.68e+00 ... (remaining 8489 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 11421 2.54 - 5.07: 99 5.07 - 7.61: 7 7.61 - 10.15: 2 10.15 - 12.69: 1 Bond angle restraints: 11530 Sorted by residual: angle pdb=" N VAL A 29 " pdb=" CA VAL A 29 " pdb=" C VAL A 29 " ideal model delta sigma weight residual 110.53 117.37 -6.84 9.40e-01 1.13e+00 5.30e+01 angle pdb=" C LEU A 30 " pdb=" N PRO A 31 " pdb=" CA PRO A 31 " ideal model delta sigma weight residual 119.05 125.60 -6.55 1.11e+00 8.12e-01 3.48e+01 angle pdb=" N PRO A 34 " pdb=" CA PRO A 34 " pdb=" CB PRO A 34 " ideal model delta sigma weight residual 103.33 109.78 -6.45 1.10e+00 8.26e-01 3.44e+01 angle pdb=" F2 BEF A1301 " pdb="BE BEF A1301 " pdb=" F3 BEF A1301 " ideal model delta sigma weight residual 119.96 107.27 12.69 3.00e+00 1.11e-01 1.79e+01 angle pdb=" N VAL A 198 " pdb=" CA VAL A 198 " pdb=" C VAL A 198 " ideal model delta sigma weight residual 113.42 108.96 4.46 1.17e+00 7.31e-01 1.45e+01 ... (remaining 11525 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 4658 17.44 - 34.87: 370 34.87 - 52.31: 50 52.31 - 69.74: 6 69.74 - 87.18: 4 Dihedral angle restraints: 5088 sinusoidal: 1922 harmonic: 3166 Sorted by residual: dihedral pdb=" N PRO A 34 " pdb=" C PRO A 34 " pdb=" CA PRO A 34 " pdb=" CB PRO A 34 " ideal model delta harmonic sigma weight residual 115.10 123.28 -8.18 0 2.50e+00 1.60e-01 1.07e+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 -87.18 87.18 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CA TYR A 516 " pdb=" C TYR A 516 " pdb=" N SER A 517 " pdb=" CA SER A 517 " ideal model delta harmonic sigma weight residual -180.00 -164.24 -15.76 0 5.00e+00 4.00e-02 9.94e+00 ... (remaining 5085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1104 0.052 - 0.104: 219 0.104 - 0.156: 28 0.156 - 0.208: 1 0.208 - 0.260: 1 Chirality restraints: 1353 Sorted by residual: chirality pdb=" CA PRO A 34 " pdb=" N PRO A 34 " pdb=" C PRO A 34 " pdb=" CB PRO A 34 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CG LEU A 73 " pdb=" CB LEU A 73 " pdb=" CD1 LEU A 73 " pdb=" CD2 LEU A 73 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CG LEU A 70 " pdb=" CB LEU A 70 " pdb=" CD1 LEU A 70 " pdb=" CD2 LEU A 70 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.15 2.00e-01 2.50e+01 6.01e-01 ... (remaining 1350 not shown) Planarity restraints: 1464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 74 " 0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO A 75 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 75 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 75 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 29 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.55e+00 pdb=" C VAL A 29 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL A 29 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU A 30 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 273 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO A 274 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 274 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 274 " 0.022 5.00e-02 4.00e+02 ... (remaining 1461 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 28 2.43 - 3.05: 5188 3.05 - 3.67: 11571 3.67 - 4.28: 16319 4.28 - 4.90: 28499 Nonbonded interactions: 61605 Sorted by model distance: nonbonded pdb=" F1 BEF A1301 " pdb="MG MG A1302 " model vdw 1.814 2.120 nonbonded pdb=" OD2 ASP A 487 " pdb=" F1 BEF A1301 " model vdw 1.884 2.990 nonbonded pdb=" OD1 ASN A 987 " pdb=" NH1 ARG A1127 " model vdw 2.249 3.120 nonbonded pdb=" O THR A 489 " pdb="MG MG A1302 " model vdw 2.275 2.170 nonbonded pdb=" OG1 THR A 751 " pdb=" OE1 GLN A 778 " model vdw 2.276 3.040 ... (remaining 61600 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: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.300 Find NCS groups from input model: 0.030 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: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 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 : 0.011 0.995 8495 Z= 1.094 Angle : 0.606 12.687 11530 Z= 0.347 Chirality : 0.042 0.260 1353 Planarity : 0.004 0.041 1464 Dihedral : 12.442 87.180 3036 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % 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: -2.38 (0.23), residues: 1082 helix: -0.21 (0.22), residues: 490 sheet: -2.82 (0.38), residues: 131 loop : -2.73 (0.24), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 175 TYR 0.014 0.001 TYR A1057 PHE 0.014 0.001 PHE A 405 TRP 0.006 0.001 TRP A1187 HIS 0.005 0.001 HIS A 672 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 8494) covalent geometry : angle 0.60556 (11530) hydrogen bonds : bond 0.15510 ( 402) hydrogen bonds : angle 5.80962 ( 1167) Misc. bond : bond 0.99535 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.292 Fit side-chains REVERT: A 695 MET cc_start: 0.8689 (ttm) cc_final: 0.8381 (ttm) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0661 time to fit residues: 5.7993 Evaluate side-chains 35 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN A 166 HIS A 196 HIS A1050 GLN ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.080731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.060325 restraints weight = 23929.494| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.39 r_work: 0.2962 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8495 Z= 0.120 Angle : 0.519 8.397 11530 Z= 0.267 Chirality : 0.040 0.144 1353 Planarity : 0.004 0.042 1464 Dihedral : 4.075 16.095 1149 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.57 % Allowed : 8.99 % Favored : 90.44 % 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: -1.09 (0.25), residues: 1082 helix: 1.04 (0.24), residues: 490 sheet: -2.61 (0.37), residues: 145 loop : -2.09 (0.26), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1048 TYR 0.010 0.001 TYR A 219 PHE 0.014 0.001 PHE A 226 TRP 0.005 0.001 TRP A1187 HIS 0.007 0.001 HIS A 672 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 8494) covalent geometry : angle 0.51893 (11530) hydrogen bonds : bond 0.04692 ( 402) hydrogen bonds : angle 4.33210 ( 1167) Misc. bond : bond 0.00173 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.299 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 43 average time/residue: 0.0641 time to fit residues: 4.5811 Evaluate side-chains 40 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 1191 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 32 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 44 optimal weight: 0.0970 chunk 43 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 64 optimal weight: 0.4980 chunk 28 optimal weight: 0.6980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 754 HIS A1129 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.081365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.060906 restraints weight = 23725.920| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 3.40 r_work: 0.2974 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 8495 Z= 0.098 Angle : 0.483 7.723 11530 Z= 0.246 Chirality : 0.039 0.137 1353 Planarity : 0.003 0.039 1464 Dihedral : 3.894 15.307 1149 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.48 % Allowed : 10.01 % Favored : 88.51 % 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: -0.43 (0.25), residues: 1082 helix: 1.60 (0.24), residues: 492 sheet: -2.28 (0.38), residues: 147 loop : -1.76 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1048 TYR 0.010 0.001 TYR A 219 PHE 0.016 0.001 PHE A 226 TRP 0.005 0.001 TRP A 787 HIS 0.006 0.000 HIS A 672 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 8494) covalent geometry : angle 0.48333 (11530) hydrogen bonds : bond 0.04072 ( 402) hydrogen bonds : angle 3.99122 ( 1167) Misc. bond : bond 0.00036 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.244 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 53 average time/residue: 0.0573 time to fit residues: 5.1023 Evaluate side-chains 42 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1191 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 23 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 78 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 97 optimal weight: 0.0370 chunk 79 optimal weight: 4.9990 overall best weight: 1.7662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.079316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.058790 restraints weight = 24494.412| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 3.43 r_work: 0.2929 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8495 Z= 0.165 Angle : 0.529 8.588 11530 Z= 0.268 Chirality : 0.040 0.149 1353 Planarity : 0.003 0.039 1464 Dihedral : 4.022 15.608 1149 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.48 % Allowed : 11.60 % Favored : 86.92 % 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: -0.17 (0.26), residues: 1082 helix: 1.83 (0.24), residues: 492 sheet: -2.16 (0.38), residues: 147 loop : -1.66 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 175 TYR 0.010 0.001 TYR A1057 PHE 0.017 0.001 PHE A 226 TRP 0.006 0.001 TRP A1187 HIS 0.008 0.001 HIS A 672 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 8494) covalent geometry : angle 0.52942 (11530) hydrogen bonds : bond 0.04564 ( 402) hydrogen bonds : angle 4.00280 ( 1167) Misc. bond : bond 0.00073 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.295 Fit side-chains REVERT: A 813 MET cc_start: 0.9074 (tpt) cc_final: 0.8734 (tpt) outliers start: 13 outliers final: 9 residues processed: 47 average time/residue: 0.0586 time to fit residues: 4.6348 Evaluate side-chains 44 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1007 SER Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1191 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 14 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 35 optimal weight: 0.0060 chunk 94 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 56 optimal weight: 0.0570 chunk 92 optimal weight: 2.9990 overall best weight: 0.7918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.080458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.059916 restraints weight = 23968.317| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 3.43 r_work: 0.2957 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 8495 Z= 0.102 Angle : 0.499 12.602 11530 Z= 0.247 Chirality : 0.039 0.149 1353 Planarity : 0.003 0.039 1464 Dihedral : 3.897 15.442 1149 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.14 % Allowed : 12.63 % Favored : 86.23 % 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 (0.26), residues: 1082 helix: 2.04 (0.24), residues: 493 sheet: -1.94 (0.39), residues: 144 loop : -1.46 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1048 TYR 0.008 0.001 TYR A1057 PHE 0.018 0.001 PHE A 226 TRP 0.006 0.001 TRP A 787 HIS 0.006 0.001 HIS A 672 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 8494) covalent geometry : angle 0.49857 (11530) hydrogen bonds : bond 0.04044 ( 402) hydrogen bonds : angle 3.87801 ( 1167) Misc. bond : bond 0.00035 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.346 Fit side-chains REVERT: A 813 MET cc_start: 0.9058 (tpt) cc_final: 0.8709 (tpt) outliers start: 10 outliers final: 7 residues processed: 45 average time/residue: 0.0595 time to fit residues: 4.6107 Evaluate side-chains 45 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1007 SER Chi-restraints excluded: chain A residue 1191 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 80 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 104 optimal weight: 0.0770 chunk 102 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 overall best weight: 1.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN A 129 GLN ** A 205 GLN ** 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 = 0.3486 r_free = 0.3486 target = 0.079074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.059029 restraints weight = 23950.795| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.32 r_work: 0.2928 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8495 Z= 0.164 Angle : 0.538 10.885 11530 Z= 0.268 Chirality : 0.040 0.152 1353 Planarity : 0.003 0.038 1464 Dihedral : 4.030 16.082 1149 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.48 % Allowed : 13.08 % Favored : 85.44 % 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: 0.20 (0.26), residues: 1082 helix: 2.11 (0.24), residues: 492 sheet: -1.95 (0.38), residues: 154 loop : -1.42 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 175 TYR 0.012 0.001 TYR A1057 PHE 0.019 0.001 PHE A 226 TRP 0.006 0.001 TRP A1187 HIS 0.008 0.001 HIS A 672 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 8494) covalent geometry : angle 0.53820 (11530) hydrogen bonds : bond 0.04575 ( 402) hydrogen bonds : angle 3.98965 ( 1167) Misc. bond : bond 0.00087 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.304 Fit side-chains REVERT: A 813 MET cc_start: 0.9057 (tpt) cc_final: 0.8753 (tpt) outliers start: 13 outliers final: 10 residues processed: 48 average time/residue: 0.0591 time to fit residues: 4.8376 Evaluate side-chains 46 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1007 SER Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1191 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 100 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 27 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 42 optimal weight: 0.0370 chunk 44 optimal weight: 0.1980 chunk 89 optimal weight: 0.2980 chunk 40 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 75 optimal weight: 5.9990 chunk 3 optimal weight: 50.0000 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.081197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.061224 restraints weight = 23882.609| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 3.34 r_work: 0.2976 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8495 Z= 0.090 Angle : 0.507 10.617 11530 Z= 0.246 Chirality : 0.038 0.148 1353 Planarity : 0.003 0.039 1464 Dihedral : 3.832 15.558 1149 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.25 % Allowed : 13.77 % Favored : 84.98 % 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: 0.52 (0.26), residues: 1082 helix: 2.25 (0.24), residues: 493 sheet: -1.41 (0.41), residues: 144 loop : -1.28 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 982 TYR 0.007 0.001 TYR A 219 PHE 0.017 0.001 PHE A 226 TRP 0.007 0.001 TRP A 787 HIS 0.006 0.001 HIS A 672 Details of bonding type rmsd covalent geometry : bond 0.00194 ( 8494) covalent geometry : angle 0.50676 (11530) hydrogen bonds : bond 0.03715 ( 402) hydrogen bonds : angle 3.83184 ( 1167) Misc. bond : bond 0.00019 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.252 Fit side-chains REVERT: A 72 MET cc_start: 0.7922 (tmm) cc_final: 0.7205 (tpp) REVERT: A 813 MET cc_start: 0.9050 (tpt) cc_final: 0.8707 (tpt) outliers start: 11 outliers final: 7 residues processed: 49 average time/residue: 0.0562 time to fit residues: 4.6277 Evaluate side-chains 45 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1007 SER Chi-restraints excluded: chain A residue 1191 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 31 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 49 optimal weight: 0.0970 chunk 3 optimal weight: 50.0000 chunk 8 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.079661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.059747 restraints weight = 23893.740| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.32 r_work: 0.2943 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8495 Z= 0.140 Angle : 0.524 10.225 11530 Z= 0.257 Chirality : 0.039 0.148 1353 Planarity : 0.003 0.038 1464 Dihedral : 3.907 15.940 1149 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.48 % Allowed : 13.54 % Favored : 84.98 % 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: 0.57 (0.26), residues: 1082 helix: 2.32 (0.24), residues: 488 sheet: -1.35 (0.41), residues: 144 loop : -1.25 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 175 TYR 0.010 0.001 TYR A1057 PHE 0.020 0.001 PHE A 226 TRP 0.005 0.001 TRP A1187 HIS 0.007 0.001 HIS A 672 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 8494) covalent geometry : angle 0.52376 (11530) hydrogen bonds : bond 0.04246 ( 402) hydrogen bonds : angle 3.88140 ( 1167) Misc. bond : bond 0.00072 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.299 Fit side-chains REVERT: A 72 MET cc_start: 0.7904 (tmm) cc_final: 0.7279 (tpp) REVERT: A 408 ILE cc_start: 0.9196 (mt) cc_final: 0.8979 (mp) REVERT: A 813 MET cc_start: 0.9066 (tpt) cc_final: 0.8765 (tpt) outliers start: 13 outliers final: 12 residues processed: 49 average time/residue: 0.0527 time to fit residues: 4.3914 Evaluate side-chains 50 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1007 SER Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1191 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 13 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 2 optimal weight: 0.0570 chunk 33 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.080589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.060721 restraints weight = 23665.512| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.32 r_work: 0.2960 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 8495 Z= 0.100 Angle : 0.503 10.110 11530 Z= 0.245 Chirality : 0.039 0.148 1353 Planarity : 0.003 0.039 1464 Dihedral : 3.825 15.417 1149 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.14 % Allowed : 14.45 % Favored : 84.41 % 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: 0.70 (0.26), residues: 1082 helix: 2.40 (0.24), residues: 489 sheet: -1.20 (0.42), residues: 144 loop : -1.18 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 247 TYR 0.008 0.001 TYR A1057 PHE 0.020 0.001 PHE A 226 TRP 0.006 0.001 TRP A 787 HIS 0.006 0.001 HIS A 672 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 8494) covalent geometry : angle 0.50294 (11530) hydrogen bonds : bond 0.03869 ( 402) hydrogen bonds : angle 3.81789 ( 1167) Misc. bond : bond 0.00023 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.225 Fit side-chains REVERT: A 408 ILE cc_start: 0.9155 (mt) cc_final: 0.8954 (mp) REVERT: A 813 MET cc_start: 0.9054 (tpt) cc_final: 0.8726 (tpt) outliers start: 10 outliers final: 9 residues processed: 47 average time/residue: 0.0516 time to fit residues: 4.0948 Evaluate side-chains 47 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1007 SER Chi-restraints excluded: chain A residue 1191 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.0050 chunk 33 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 chunk 84 optimal weight: 0.2980 chunk 43 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 6 optimal weight: 0.0060 overall best weight: 0.3810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.084771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.063480 restraints weight = 24089.639| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.30 r_work: 0.2990 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 8495 Z= 0.089 Angle : 0.505 10.204 11530 Z= 0.243 Chirality : 0.038 0.146 1353 Planarity : 0.003 0.038 1464 Dihedral : 3.723 15.581 1149 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.02 % Allowed : 14.68 % Favored : 84.30 % 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: 0.85 (0.26), residues: 1082 helix: 2.50 (0.24), residues: 489 sheet: -0.99 (0.43), residues: 144 loop : -1.14 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 634 TYR 0.006 0.001 TYR A1057 PHE 0.020 0.001 PHE A 226 TRP 0.007 0.001 TRP A 787 HIS 0.005 0.000 HIS A 672 Details of bonding type rmsd covalent geometry : bond 0.00194 ( 8494) covalent geometry : angle 0.50491 (11530) hydrogen bonds : bond 0.03534 ( 402) hydrogen bonds : angle 3.75394 ( 1167) Misc. bond : bond 0.00014 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.296 Fit side-chains REVERT: A 72 MET cc_start: 0.7901 (tmm) cc_final: 0.7324 (tpp) REVERT: A 408 ILE cc_start: 0.9118 (mt) cc_final: 0.8917 (mp) REVERT: A 813 MET cc_start: 0.9059 (tpt) cc_final: 0.8703 (tpt) outliers start: 9 outliers final: 8 residues processed: 51 average time/residue: 0.0581 time to fit residues: 4.9875 Evaluate side-chains 49 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1007 SER Chi-restraints excluded: chain A residue 1191 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 31 optimal weight: 0.3980 chunk 86 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 3 optimal weight: 50.0000 chunk 10 optimal weight: 0.6980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.079483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.059450 restraints weight = 23770.410| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.32 r_work: 0.2932 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8495 Z= 0.155 Angle : 0.529 9.943 11530 Z= 0.262 Chirality : 0.040 0.148 1353 Planarity : 0.003 0.037 1464 Dihedral : 3.899 16.158 1149 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.37 % Allowed : 14.45 % Favored : 84.19 % 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: 0.79 (0.26), residues: 1082 helix: 2.48 (0.24), residues: 489 sheet: -1.16 (0.42), residues: 149 loop : -1.15 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 175 TYR 0.012 0.001 TYR A1057 PHE 0.020 0.001 PHE A 226 TRP 0.005 0.001 TRP A 137 HIS 0.007 0.001 HIS A 672 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 8494) covalent geometry : angle 0.52900 (11530) hydrogen bonds : bond 0.04319 ( 402) hydrogen bonds : angle 3.86180 ( 1167) Misc. bond : bond 0.00045 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1670.76 seconds wall clock time: 29 minutes 17.47 seconds (1757.47 seconds total)