Starting phenix.real_space_refine on Fri Aug 22 23:12:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xmu_22264/08_2025/6xmu_22264.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xmu_22264/08_2025/6xmu_22264.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/6xmu_22264/08_2025/6xmu_22264.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xmu_22264/08_2025/6xmu_22264.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xmu_22264/08_2025/6xmu_22264.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xmu_22264/08_2025/6xmu_22264.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= 0.002 sd= 0.030 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 5422 2.51 5 N 1398 2.21 5 O 1548 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 26 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8411 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1090, 8306 Classifications: {'peptide': 1090} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 49, 'TRANS': 1040} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 326 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'PHE:plan': 4, 'TYR:plan': 4, 'GLN:plan1': 3, 'GLU:plan': 14, 'TRP:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 176 Chain: "B" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 100 Classifications: {'peptide': 20} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'TRANS': 19} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'UNK:plan-1': 20} Unresolved non-hydrogen planarities: 20 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: 1.46, per 1000 atoms: 0.17 Number of scatterers: 8411 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 1548 8.00 N 1398 7.00 C 5422 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: 0.61 Conformation dependent library (CDL) restraints added in 286.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2088 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 47.7% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 28 through 44 removed outlier: 3.793A pdb=" N PHE A 32 " --> pdb=" O TYR A 28 " (cutoff:3.500A) removed outlier: 4.082A 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 73 removed outlier: 3.539A pdb=" N LEU A 61 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 86 Processing helix chain 'A' and resid 156 through 162 removed outlier: 3.663A pdb=" N PHE A 160 " --> pdb=" O LYS A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 188 through 197 removed outlier: 4.215A pdb=" N GLU A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N HIS A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 214 Processing helix chain 'A' and resid 218 through 247 Processing helix chain 'A' and resid 332 through 336 removed outlier: 4.322A pdb=" N ILE A 336 " --> pdb=" O VAL A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 375 removed outlier: 3.620A 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 425 removed outlier: 4.075A pdb=" N LEU A 400 " --> pdb=" O ASN A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 441 removed outlier: 3.540A pdb=" N LEU A 431 " --> pdb=" O ILE A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 463 Processing helix chain 'A' and resid 471 through 480 removed outlier: 3.841A pdb=" N ILE A 475 " --> pdb=" O PRO A 472 " (cutoff:3.500A) Proline residue: A 476 - end of helix removed outlier: 3.531A pdb=" N GLY A 479 " --> pdb=" O PRO A 476 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG A 480 " --> pdb=" O PHE A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 532 removed outlier: 3.790A 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 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 773 Processing helix chain 'A' and resid 778 through 784 Processing helix chain 'A' and resid 796 through 807 Processing helix chain 'A' and resid 820 through 827 Processing helix chain 'A' and resid 837 through 852 Processing helix chain 'A' and resid 971 through 1010 removed outlier: 4.349A pdb=" N THR A 975 " --> pdb=" O VAL A 971 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N CYS A 983 " --> pdb=" O ARG A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1037 removed outlier: 3.889A pdb=" N LEU A1027 " --> pdb=" O VAL A1023 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER A1036 " --> pdb=" O PHE A1032 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ARG A1037 " --> pdb=" O LEU A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1084 removed outlier: 3.779A pdb=" N MET A1059 " --> pdb=" O ASN A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1119 removed outlier: 3.930A pdb=" N THR A1103 " --> pdb=" O SER A1099 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE A1108 " --> pdb=" O GLY A1104 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE A1117 " --> pdb=" O GLN A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1132 Processing helix chain 'A' and resid 1133 through 1152 removed outlier: 3.513A 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 1168 through 1197 removed outlier: 3.638A pdb=" N LYS A1172 " --> pdb=" O THR A1168 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 20 Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 8 removed outlier: 3.513A pdb=" N VAL A 143 " --> pdb=" O HIS A 138 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU A 136 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE A 128 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 87 through 88 removed outlier: 6.762A pdb=" N TYR A 102 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER A 15 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU A 100 " --> pdb=" O SER A 15 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N LEU A 17 " --> pdb=" O HIS A 98 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N HIS A 98 " --> pdb=" O LEU A 17 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA4, first strand: chain 'A' and resid 264 through 267 removed outlier: 4.845A pdb=" N ASN A 257 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LEU A 277 " --> pdb=" O PHE A 259 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ASP A 292 " --> pdb=" O THR A 370 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 299 through 303 removed outlier: 6.690A pdb=" N SER A 299 " --> pdb=" O VAL A 348 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL A 348 " --> pdb=" O SER A 299 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE A 301 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.589A 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: 6.518A pdb=" N GLY A 830 " --> pdb=" O PHE A 964 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N SER A 966 " --> pdb=" O GLY A 830 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ALA A 832 " --> pdb=" O SER A 966 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N THR A 811 " --> pdb=" O VAL A 829 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N ILE A 831 " --> pdb=" O THR A 811 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N MET A 813 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N LEU A 833 " --> pdb=" O MET A 813 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLY A 815 " --> pdb=" O LEU A 833 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL A 483 " --> pdb=" O LEU A 812 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N CYS A 814 " --> pdb=" O VAL A 483 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 498 through 501 removed outlier: 6.852A pdb=" N ILE A 670 " --> pdb=" O GLU A 500 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 536 through 537 removed outlier: 3.827A pdb=" N VAL A 536 " --> pdb=" O VAL A 544 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 544 " --> pdb=" O VAL A 536 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 575 through 579 removed outlier: 6.886A pdb=" N ILE A 592 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE A 600 " --> pdb=" O ALA A 593 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LEU A 638 " --> pdb=" O ASN A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 695 through 696 removed outlier: 6.600A pdb=" N MET A 695 " --> pdb=" O TYR A 789 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL A 788 " --> pdb=" O ILE A 763 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP A 722 " --> pdb=" O LEU A 733 " (cutoff:3.500A) 409 hydrogen bonds defined for protein. 1191 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: 1.07 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2701 1.34 - 1.46: 1481 1.46 - 1.57: 4335 1.57 - 1.69: 0 1.69 - 1.81: 63 Bond restraints: 8580 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 1.76e+01 bond pdb=" F3 BEF A1301 " pdb="BE BEF A1301 " ideal model delta sigma weight residual 1.476 1.543 -0.067 2.00e-02 2.50e+03 1.14e+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 8.54e+00 bond pdb=" N VAL A 29 " pdb=" CA VAL A 29 " ideal model delta sigma weight residual 1.460 1.486 -0.026 1.19e-02 7.06e+03 4.64e+00 bond pdb=" CA VAL A 29 " pdb=" C VAL A 29 " ideal model delta sigma weight residual 1.524 1.547 -0.023 1.23e-02 6.61e+03 3.56e+00 ... (remaining 8575 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 11549 2.55 - 5.10: 84 5.10 - 7.64: 11 7.64 - 10.19: 2 10.19 - 12.74: 1 Bond angle restraints: 11647 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 110.53 117.10 -6.57 9.40e-01 1.13e+00 4.88e+01 angle pdb=" C LEU A 30 " pdb=" N PRO A 31 " pdb=" CA PRO A 31 " ideal model delta sigma weight residual 118.85 126.10 -7.25 1.09e+00 8.42e-01 4.43e+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=" C LYS A 26 " pdb=" N PRO A 27 " pdb=" CA PRO A 27 " ideal model delta sigma weight residual 119.05 125.22 -6.17 1.11e+00 8.12e-01 3.09e+01 angle pdb=" F2 BEF A1301 " pdb="BE BEF A1301 " pdb=" F3 BEF A1301 " ideal model delta sigma weight residual 119.96 107.22 12.74 3.00e+00 1.11e-01 1.80e+01 ... (remaining 11642 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4791 17.94 - 35.88: 302 35.88 - 53.81: 38 53.81 - 71.75: 6 71.75 - 89.69: 4 Dihedral angle restraints: 5141 sinusoidal: 1922 harmonic: 3219 Sorted by residual: dihedral pdb=" CA TYR A 761 " pdb=" C TYR A 761 " pdb=" N ASP A 762 " pdb=" CA ASP A 762 " ideal model delta harmonic sigma weight residual 180.00 160.37 19.63 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA TYR A1121 " pdb=" C TYR A1121 " pdb=" N GLN A1122 " pdb=" CA GLN A1122 " ideal model delta harmonic sigma weight residual -180.00 -161.29 -18.71 0 5.00e+00 4.00e-02 1.40e+01 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 115.10 123.27 -8.17 0 2.50e+00 1.60e-01 1.07e+01 ... (remaining 5138 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1140 0.052 - 0.105: 194 0.105 - 0.157: 32 0.157 - 0.210: 2 0.210 - 0.262: 3 Chirality restraints: 1371 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 1.72e+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 -2.37 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CG LEU A 30 " pdb=" CB LEU A 30 " pdb=" CD1 LEU A 30 " pdb=" CD2 LEU A 30 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 1368 not shown) Planarity restraints: 1478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 29 " -0.010 2.00e-02 2.50e+03 1.93e-02 3.74e+00 pdb=" C VAL A 29 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL A 29 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU A 30 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 30 " 0.028 5.00e-02 4.00e+02 4.25e-02 2.89e+00 pdb=" N PRO A 31 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 31 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 31 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1006 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.81e+00 pdb=" C LEU A1006 " -0.029 2.00e-02 2.50e+03 pdb=" O LEU A1006 " 0.011 2.00e-02 2.50e+03 pdb=" N SER A1007 " 0.010 2.00e-02 2.50e+03 ... (remaining 1475 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.54: 40 2.54 - 3.13: 6505 3.13 - 3.72: 12155 3.72 - 4.31: 16017 4.31 - 4.90: 28123 Nonbonded interactions: 62840 Sorted by model distance: nonbonded pdb=" F1 BEF A1301 " pdb="MG MG A1302 " model vdw 1.956 2.120 nonbonded pdb=" OD2 ASP A 487 " pdb=" F1 BEF A1301 " model vdw 1.959 2.990 nonbonded pdb=" OD2 ASP A 487 " pdb="MG MG A1302 " model vdw 2.194 2.170 nonbonded pdb=" OG SER A 506 " pdb=" OH TYR A 516 " model vdw 2.237 3.040 nonbonded pdb=" OG SER A1099 " pdb=" OD1 ASN A1102 " model vdw 2.241 3.040 ... (remaining 62835 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.150 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: 0.090 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 7.010 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 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 : 0.012 1.013 8581 Z= 1.107 Angle : 0.585 12.740 11647 Z= 0.329 Chirality : 0.042 0.262 1371 Planarity : 0.004 0.042 1478 Dihedral : 11.801 89.690 3053 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % 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 aren not related in a simple way. whole: -2.43 (0.22), residues: 1080 helix: 0.00 (0.22), residues: 478 sheet: -2.86 (0.40), residues: 120 loop : -3.02 (0.21), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 630 TYR 0.009 0.001 TYR A 761 PHE 0.017 0.001 PHE A 405 TRP 0.005 0.001 TRP A 77 HIS 0.005 0.001 HIS A 672 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 8580) covalent geometry : angle 0.58497 (11647) hydrogen bonds : bond 0.14855 ( 409) hydrogen bonds : angle 5.23499 ( 1191) Misc. bond : bond 1.01335 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.240 Fit side-chains REVERT: A 207 PHE cc_start: 0.8589 (t80) cc_final: 0.8352 (t80) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.0619 time to fit residues: 4.8939 Evaluate side-chains 37 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 20.0000 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN A 107 ASN ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 HIS A 990 GLN A1050 GLN A1122 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.075638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.054486 restraints weight = 29039.032| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 3.24 r_work: 0.2937 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 8581 Z= 0.205 Angle : 0.568 7.989 11647 Z= 0.288 Chirality : 0.041 0.166 1371 Planarity : 0.004 0.040 1478 Dihedral : 4.067 20.769 1167 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.68 % Allowed : 9.90 % Favored : 89.42 % 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 aren not related in a simple way. whole: -1.33 (0.25), residues: 1080 helix: 1.12 (0.24), residues: 488 sheet: -2.88 (0.33), residues: 163 loop : -2.47 (0.24), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 260 TYR 0.009 0.001 TYR A 761 PHE 0.022 0.002 PHE A 226 TRP 0.004 0.001 TRP A 218 HIS 0.006 0.001 HIS A 672 Details of bonding type rmsd covalent geometry : bond 0.00486 ( 8580) covalent geometry : angle 0.56765 (11647) hydrogen bonds : bond 0.04862 ( 409) hydrogen bonds : angle 4.14152 ( 1191) Misc. bond : bond 0.00117 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.197 Fit side-chains REVERT: A 72 MET cc_start: 0.7134 (tmm) cc_final: 0.6840 (tpp) REVERT: A 207 PHE cc_start: 0.9152 (t80) cc_final: 0.8820 (t80) REVERT: A 213 LEU cc_start: 0.8912 (tp) cc_final: 0.8530 (pp) REVERT: A 1011 MET cc_start: 0.8320 (mmp) cc_final: 0.8088 (mmp) REVERT: A 1181 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8813 (mm) outliers start: 6 outliers final: 3 residues processed: 41 average time/residue: 0.0505 time to fit residues: 3.4262 Evaluate side-chains 41 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1180 LEU Chi-restraints excluded: chain A residue 1181 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 68 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 30 optimal weight: 30.0000 chunk 3 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 84 optimal weight: 0.0870 chunk 39 optimal weight: 9.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 HIS ** A 205 GLN ** 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 = 0.3608 r_free = 0.3608 target = 0.077057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.055921 restraints weight = 28719.939| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 3.43 r_work: 0.2963 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8581 Z= 0.098 Angle : 0.479 7.399 11647 Z= 0.242 Chirality : 0.039 0.178 1371 Planarity : 0.003 0.033 1478 Dihedral : 3.748 20.451 1167 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.14 % Allowed : 11.49 % Favored : 87.37 % 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 aren not related in a simple way. whole: -0.69 (0.25), residues: 1080 helix: 1.62 (0.24), residues: 489 sheet: -2.43 (0.35), residues: 163 loop : -2.16 (0.25), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1048 TYR 0.006 0.001 TYR A 761 PHE 0.023 0.001 PHE A 204 TRP 0.004 0.001 TRP A 218 HIS 0.006 0.001 HIS A 672 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 8580) covalent geometry : angle 0.47938 (11647) hydrogen bonds : bond 0.04034 ( 409) hydrogen bonds : angle 3.78132 ( 1191) Misc. bond : bond 0.00047 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.287 Fit side-chains REVERT: A 72 MET cc_start: 0.7155 (tmm) cc_final: 0.6807 (tpp) REVERT: A 207 PHE cc_start: 0.9117 (t80) cc_final: 0.8784 (t80) REVERT: A 213 LEU cc_start: 0.8928 (tp) cc_final: 0.8534 (pp) REVERT: A 424 MET cc_start: 0.8658 (tpp) cc_final: 0.8292 (tmm) REVERT: A 449 MET cc_start: 0.7876 (ptp) cc_final: 0.7647 (ptm) REVERT: A 1181 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8695 (mm) outliers start: 10 outliers final: 4 residues processed: 48 average time/residue: 0.0540 time to fit residues: 4.2696 Evaluate side-chains 42 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1180 LEU Chi-restraints excluded: chain A residue 1181 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 14 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 97 optimal weight: 0.0970 chunk 80 optimal weight: 4.9990 chunk 110 optimal weight: 30.0000 chunk 54 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.074908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.054130 restraints weight = 29330.545| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 3.23 r_work: 0.2918 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 8581 Z= 0.217 Angle : 0.566 14.447 11647 Z= 0.284 Chirality : 0.041 0.173 1371 Planarity : 0.003 0.040 1478 Dihedral : 4.001 20.735 1167 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.25 % Allowed : 14.22 % Favored : 84.53 % 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 aren not related in a simple way. whole: -0.39 (0.26), residues: 1080 helix: 1.83 (0.24), residues: 494 sheet: -2.20 (0.38), residues: 149 loop : -2.06 (0.25), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 260 TYR 0.009 0.001 TYR A 761 PHE 0.018 0.002 PHE A 226 TRP 0.005 0.001 TRP A 77 HIS 0.006 0.001 HIS A 672 Details of bonding type rmsd covalent geometry : bond 0.00514 ( 8580) covalent geometry : angle 0.56579 (11647) hydrogen bonds : bond 0.04749 ( 409) hydrogen bonds : angle 3.92066 ( 1191) Misc. bond : bond 0.00109 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: A 207 PHE cc_start: 0.9190 (t80) cc_final: 0.8895 (t80) REVERT: A 213 LEU cc_start: 0.8865 (tp) cc_final: 0.8450 (pp) REVERT: A 424 MET cc_start: 0.8720 (tpp) cc_final: 0.8354 (tmm) REVERT: A 433 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8988 (pp) REVERT: A 453 MET cc_start: 0.8517 (mtt) cc_final: 0.8007 (mtt) REVERT: A 1000 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8633 (mp) REVERT: A 1011 MET cc_start: 0.8124 (mmp) cc_final: 0.7908 (mmp) REVERT: A 1181 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8821 (mm) outliers start: 11 outliers final: 6 residues processed: 47 average time/residue: 0.0505 time to fit residues: 3.8027 Evaluate side-chains 46 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1168 THR Chi-restraints excluded: chain A residue 1180 LEU Chi-restraints excluded: chain A residue 1181 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 110 optimal weight: 30.0000 chunk 101 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 68 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 GLN ** 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 = 0.3582 r_free = 0.3582 target = 0.075587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.054507 restraints weight = 29209.274| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 3.48 r_work: 0.2919 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8581 Z= 0.147 Angle : 0.498 12.189 11647 Z= 0.251 Chirality : 0.040 0.184 1371 Planarity : 0.003 0.037 1478 Dihedral : 3.849 20.934 1167 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.37 % Allowed : 15.70 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.26), residues: 1080 helix: 2.05 (0.24), residues: 489 sheet: -1.94 (0.38), residues: 155 loop : -1.95 (0.26), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 260 TYR 0.007 0.001 TYR A 761 PHE 0.019 0.001 PHE A 226 TRP 0.005 0.001 TRP A 415 HIS 0.006 0.001 HIS A 672 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 8580) covalent geometry : angle 0.49794 (11647) hydrogen bonds : bond 0.04216 ( 409) hydrogen bonds : angle 3.72106 ( 1191) Misc. bond : bond 0.00069 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: A 207 PHE cc_start: 0.9157 (t80) cc_final: 0.8855 (t80) REVERT: A 213 LEU cc_start: 0.8916 (tp) cc_final: 0.8478 (pp) REVERT: A 424 MET cc_start: 0.8872 (tpp) cc_final: 0.8471 (tmm) REVERT: A 449 MET cc_start: 0.7832 (ptp) cc_final: 0.6868 (ptm) REVERT: A 453 MET cc_start: 0.8512 (mtt) cc_final: 0.7950 (mtt) REVERT: A 638 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8071 (pp) REVERT: A 1011 MET cc_start: 0.8317 (mmp) cc_final: 0.8096 (mmp) REVERT: A 1136 MET cc_start: 0.6743 (tmm) cc_final: 0.6385 (tmm) REVERT: A 1181 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8807 (mm) outliers start: 12 outliers final: 7 residues processed: 49 average time/residue: 0.0520 time to fit residues: 4.2603 Evaluate side-chains 47 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1180 LEU Chi-restraints excluded: chain A residue 1181 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 6.9990 chunk 31 optimal weight: 0.0970 chunk 103 optimal weight: 0.9990 chunk 34 optimal weight: 0.0570 chunk 68 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 100 optimal weight: 0.6980 chunk 4 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.5700 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.076457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.055336 restraints weight = 29056.071| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 3.41 r_work: 0.2963 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8581 Z= 0.087 Angle : 0.459 11.237 11647 Z= 0.229 Chirality : 0.039 0.196 1371 Planarity : 0.003 0.034 1478 Dihedral : 3.596 20.553 1167 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.37 % Allowed : 16.15 % Favored : 82.48 % 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 aren not related in a simple way. whole: 0.20 (0.26), residues: 1080 helix: 2.28 (0.24), residues: 489 sheet: -1.66 (0.40), residues: 155 loop : -1.76 (0.26), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1048 TYR 0.005 0.001 TYR A 789 PHE 0.020 0.001 PHE A 226 TRP 0.005 0.001 TRP A 218 HIS 0.005 0.000 HIS A 672 Details of bonding type rmsd covalent geometry : bond 0.00185 ( 8580) covalent geometry : angle 0.45910 (11647) hydrogen bonds : bond 0.03640 ( 409) hydrogen bonds : angle 3.52737 ( 1191) Misc. bond : bond 0.00021 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 207 PHE cc_start: 0.9131 (t80) cc_final: 0.8818 (t80) REVERT: A 213 LEU cc_start: 0.8829 (tp) cc_final: 0.8509 (pp) REVERT: A 424 MET cc_start: 0.8793 (tpp) cc_final: 0.8441 (tmm) REVERT: A 433 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.9027 (pp) REVERT: A 449 MET cc_start: 0.7902 (ptp) cc_final: 0.6985 (ptm) REVERT: A 453 MET cc_start: 0.8518 (mtt) cc_final: 0.7987 (mtt) REVERT: A 638 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8166 (pp) REVERT: A 1181 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8827 (mm) outliers start: 12 outliers final: 4 residues processed: 48 average time/residue: 0.0499 time to fit residues: 3.9433 Evaluate side-chains 45 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1180 LEU Chi-restraints excluded: chain A residue 1181 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 87 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 92 optimal weight: 0.3980 chunk 45 optimal weight: 0.6980 chunk 99 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 30 optimal weight: 0.0980 chunk 108 optimal weight: 0.0970 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 GLN ** 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 = 0.3606 r_free = 0.3606 target = 0.077214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.056107 restraints weight = 29271.401| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.41 r_work: 0.2982 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8581 Z= 0.082 Angle : 0.465 10.362 11647 Z= 0.227 Chirality : 0.039 0.231 1371 Planarity : 0.003 0.032 1478 Dihedral : 3.447 19.698 1167 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.14 % Allowed : 16.61 % Favored : 82.25 % 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 aren not related in a simple way. whole: 0.54 (0.26), residues: 1080 helix: 2.45 (0.24), residues: 491 sheet: -1.37 (0.41), residues: 155 loop : -1.50 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 175 TYR 0.004 0.001 TYR A 761 PHE 0.022 0.001 PHE A 226 TRP 0.005 0.000 TRP A 218 HIS 0.005 0.001 HIS A 672 Details of bonding type rmsd covalent geometry : bond 0.00170 ( 8580) covalent geometry : angle 0.46492 (11647) hydrogen bonds : bond 0.03325 ( 409) hydrogen bonds : angle 3.38373 ( 1191) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: A 207 PHE cc_start: 0.9118 (t80) cc_final: 0.8812 (t80) REVERT: A 338 VAL cc_start: 0.9551 (OUTLIER) cc_final: 0.9212 (m) REVERT: A 424 MET cc_start: 0.8783 (tpp) cc_final: 0.8443 (tmm) REVERT: A 433 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.9024 (pp) REVERT: A 453 MET cc_start: 0.8533 (mtt) cc_final: 0.8007 (mtt) REVERT: A 638 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8114 (pp) REVERT: A 1181 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8847 (mm) outliers start: 10 outliers final: 6 residues processed: 44 average time/residue: 0.0550 time to fit residues: 4.0084 Evaluate side-chains 46 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1180 LEU Chi-restraints excluded: chain A residue 1181 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 38 optimal weight: 8.9990 chunk 89 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 110 optimal weight: 30.0000 chunk 67 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.075244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.054679 restraints weight = 28904.273| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.20 r_work: 0.2939 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8581 Z= 0.173 Angle : 0.517 10.449 11647 Z= 0.257 Chirality : 0.040 0.199 1371 Planarity : 0.003 0.035 1478 Dihedral : 3.701 20.345 1167 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.48 % Allowed : 16.72 % Favored : 81.80 % 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 aren not related in a simple way. whole: 0.53 (0.26), residues: 1080 helix: 2.46 (0.24), residues: 495 sheet: -1.35 (0.41), residues: 155 loop : -1.59 (0.26), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 260 TYR 0.009 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 0.00410 ( 8580) covalent geometry : angle 0.51709 (11647) hydrogen bonds : bond 0.04189 ( 409) hydrogen bonds : angle 3.59345 ( 1191) Misc. bond : bond 0.00064 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: A 207 PHE cc_start: 0.9158 (t80) cc_final: 0.8876 (t80) REVERT: A 213 LEU cc_start: 0.8837 (tp) cc_final: 0.8477 (pp) REVERT: A 338 VAL cc_start: 0.9504 (OUTLIER) cc_final: 0.9154 (m) REVERT: A 424 MET cc_start: 0.8844 (tpp) cc_final: 0.8534 (tmm) REVERT: A 433 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.9035 (pp) REVERT: A 449 MET cc_start: 0.7763 (ptp) cc_final: 0.6997 (ptm) REVERT: A 453 MET cc_start: 0.8595 (mtt) cc_final: 0.8082 (mtt) REVERT: A 638 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8260 (pp) REVERT: A 1136 MET cc_start: 0.6876 (tmm) cc_final: 0.6429 (tmm) REVERT: A 1181 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8848 (mm) outliers start: 13 outliers final: 7 residues processed: 49 average time/residue: 0.0501 time to fit residues: 4.0691 Evaluate side-chains 48 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1180 LEU Chi-restraints excluded: chain A residue 1181 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 106 optimal weight: 7.9990 chunk 5 optimal weight: 20.0000 chunk 53 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 72 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 75 optimal weight: 0.0050 chunk 37 optimal weight: 0.6980 overall best weight: 1.0596 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.075994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.054921 restraints weight = 29164.709| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 3.42 r_work: 0.2947 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8581 Z= 0.103 Angle : 0.481 10.302 11647 Z= 0.236 Chirality : 0.039 0.211 1371 Planarity : 0.003 0.034 1478 Dihedral : 3.575 20.657 1167 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.25 % Allowed : 16.84 % Favored : 81.91 % 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 aren not related in a simple way. whole: 0.70 (0.26), residues: 1080 helix: 2.56 (0.24), residues: 491 sheet: -1.22 (0.41), residues: 155 loop : -1.42 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 260 TYR 0.006 0.001 TYR A 761 PHE 0.019 0.001 PHE A 226 TRP 0.004 0.001 TRP A 218 HIS 0.006 0.001 HIS A 672 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 8580) covalent geometry : angle 0.48097 (11647) hydrogen bonds : bond 0.03740 ( 409) hydrogen bonds : angle 3.47799 ( 1191) Misc. bond : bond 0.00034 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: A 207 PHE cc_start: 0.9140 (t80) cc_final: 0.8854 (t80) REVERT: A 338 VAL cc_start: 0.9514 (OUTLIER) cc_final: 0.9168 (m) REVERT: A 424 MET cc_start: 0.8883 (tpp) cc_final: 0.8540 (tmm) REVERT: A 433 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.9031 (pp) REVERT: A 449 MET cc_start: 0.7729 (ptp) cc_final: 0.6975 (ptm) REVERT: A 453 MET cc_start: 0.8602 (mtt) cc_final: 0.8070 (mtt) REVERT: A 638 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8080 (pp) REVERT: A 1181 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8793 (mm) outliers start: 11 outliers final: 6 residues processed: 46 average time/residue: 0.0456 time to fit residues: 3.5197 Evaluate side-chains 47 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1180 LEU Chi-restraints excluded: chain A residue 1181 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.3980 chunk 67 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 GLN ** 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 = 0.3578 r_free = 0.3578 target = 0.075605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.054587 restraints weight = 29063.953| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 3.43 r_work: 0.2930 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8581 Z= 0.135 Angle : 0.496 10.201 11647 Z= 0.245 Chirality : 0.040 0.203 1371 Planarity : 0.003 0.035 1478 Dihedral : 3.629 20.599 1167 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.37 % Allowed : 16.95 % Favored : 81.68 % 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 aren not related in a simple way. whole: 0.69 (0.26), residues: 1080 helix: 2.52 (0.24), residues: 497 sheet: -1.20 (0.41), residues: 155 loop : -1.46 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 260 TYR 0.008 0.001 TYR A1057 PHE 0.021 0.001 PHE A 226 TRP 0.004 0.001 TRP A 218 HIS 0.006 0.001 HIS A 672 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 8580) covalent geometry : angle 0.49551 (11647) hydrogen bonds : bond 0.03968 ( 409) hydrogen bonds : angle 3.55611 ( 1191) Misc. bond : bond 0.00048 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: A 207 PHE cc_start: 0.9152 (t80) cc_final: 0.8876 (t80) REVERT: A 213 LEU cc_start: 0.8855 (tp) cc_final: 0.8484 (pp) REVERT: A 338 VAL cc_start: 0.9509 (OUTLIER) cc_final: 0.9165 (m) REVERT: A 424 MET cc_start: 0.8899 (tpp) cc_final: 0.8544 (tmm) REVERT: A 433 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.9034 (pp) REVERT: A 453 MET cc_start: 0.8638 (mtt) cc_final: 0.8109 (mtt) REVERT: A 638 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8097 (pp) REVERT: A 1136 MET cc_start: 0.6833 (tmm) cc_final: 0.6369 (tmm) REVERT: A 1181 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8798 (mm) outliers start: 12 outliers final: 8 residues processed: 47 average time/residue: 0.0491 time to fit residues: 3.8473 Evaluate side-chains 50 residues out of total 941 (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 74 MET Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1180 LEU Chi-restraints excluded: chain A residue 1181 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 20 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 82 optimal weight: 20.0000 chunk 63 optimal weight: 0.4980 chunk 88 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- 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 = 0.3568 r_free = 0.3568 target = 0.075043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.054439 restraints weight = 28780.492| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 3.19 r_work: 0.2931 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8581 Z= 0.164 Angle : 0.520 10.379 11647 Z= 0.258 Chirality : 0.040 0.199 1371 Planarity : 0.003 0.035 1478 Dihedral : 3.775 21.006 1167 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.48 % Allowed : 16.72 % Favored : 81.80 % 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 aren not related in a simple way. whole: 0.68 (0.26), residues: 1080 helix: 2.50 (0.24), residues: 497 sheet: -1.18 (0.42), residues: 155 loop : -1.46 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 260 TYR 0.009 0.001 TYR A1057 PHE 0.019 0.001 PHE A 204 TRP 0.004 0.001 TRP A 137 HIS 0.006 0.001 HIS A 672 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 8580) covalent geometry : angle 0.52047 (11647) hydrogen bonds : bond 0.04247 ( 409) hydrogen bonds : angle 3.64026 ( 1191) Misc. bond : bond 0.00054 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1425.88 seconds wall clock time: 25 minutes 6.23 seconds (1506.23 seconds total)