Starting phenix.real_space_refine on Thu Mar 13 01:35:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xmu_22264/03_2025/6xmu_22264.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xmu_22264/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6xmu_22264/03_2025/6xmu_22264.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xmu_22264/03_2025/6xmu_22264.map" model { file = "/net/cci-nas-00/data/ceres_data/6xmu_22264/03_2025/6xmu_22264.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xmu_22264/03_2025/6xmu_22264.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 14, '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: 5.27, per 1000 atoms: 0.63 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: 2.25 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.04 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: 2.97 Time building geometry restraints manager: 2.64 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: 1.190 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.030 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.710 ------------------------------------------------------------------------------- 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 : 0.004 0.084 8580 Z= 0.240 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.005 0.001 TRP A 77 HIS 0.005 0.001 HIS A 672 PHE 0.017 0.001 PHE A 405 TYR 0.009 0.001 TYR A 761 ARG 0.003 0.000 ARG A 630 *********************** 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 : 0.950 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: 0.1961 time to fit residues: 15.5797 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 : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 = 0.3576 r_free = 0.3576 target = 0.075938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.054751 restraints weight = 28933.575| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.36 r_work: 0.2936 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.0916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8580 Z= 0.295 Angle : 0.554 8.044 11647 Z= 0.281 Chirality : 0.041 0.176 1371 Planarity : 0.004 0.039 1478 Dihedral : 3.992 20.507 1167 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.68 % Allowed : 9.22 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.24), residues: 1080 helix: 1.06 (0.24), residues: 488 sheet: -2.81 (0.36), residues: 144 loop : -2.49 (0.24), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 415 HIS 0.006 0.001 HIS A 672 PHE 0.020 0.001 PHE A 226 TYR 0.009 0.001 TYR A 761 ARG 0.003 0.000 ARG A1127 *********************** 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 : 0.863 Fit side-chains revert: symmetry clash REVERT: A 207 PHE cc_start: 0.9128 (t80) cc_final: 0.8788 (t80) REVERT: A 213 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8485 (pp) REVERT: A 1181 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8838 (mm) outliers start: 6 outliers final: 2 residues processed: 41 average time/residue: 0.1485 time to fit residues: 10.1239 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 : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU 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 87 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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** A 595 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.075640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.054273 restraints weight = 29582.869| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 3.34 r_work: 0.2921 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8580 Z= 0.280 Angle : 0.531 7.626 11647 Z= 0.270 Chirality : 0.041 0.170 1371 Planarity : 0.003 0.039 1478 Dihedral : 3.990 20.724 1167 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.37 % Allowed : 12.29 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.25), residues: 1080 helix: 1.58 (0.24), residues: 488 sheet: -2.52 (0.34), residues: 163 loop : -2.28 (0.25), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 415 HIS 0.006 0.001 HIS A 672 PHE 0.024 0.002 PHE A 204 TYR 0.009 0.001 TYR A 761 ARG 0.002 0.000 ARG A 260 *********************** 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 50 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: A 207 PHE cc_start: 0.9174 (t80) cc_final: 0.8851 (t80) REVERT: A 213 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8518 (pp) REVERT: A 424 MET cc_start: 0.8620 (tpp) cc_final: 0.8311 (tmm) REVERT: A 1181 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8819 (mm) outliers start: 12 outliers final: 4 residues processed: 47 average time/residue: 0.1471 time to fit residues: 11.5627 Evaluate side-chains 42 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 829 VAL 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 58 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3597 r_free = 0.3597 target = 0.076543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.055363 restraints weight = 28985.779| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.45 r_work: 0.2949 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8580 Z= 0.157 Angle : 0.481 12.583 11647 Z= 0.240 Chirality : 0.039 0.190 1371 Planarity : 0.003 0.035 1478 Dihedral : 3.715 20.518 1167 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.02 % Allowed : 13.88 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.26), residues: 1080 helix: 1.92 (0.24), residues: 489 sheet: -2.18 (0.36), residues: 162 loop : -1.96 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 218 HIS 0.005 0.001 HIS A 672 PHE 0.020 0.001 PHE A 226 TYR 0.006 0.001 TYR A 761 ARG 0.001 0.000 ARG A1048 *********************** 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: 9 poor density : 40 time to evaluate : 1.052 Fit side-chains revert: symmetry clash REVERT: A 207 PHE cc_start: 0.9141 (t80) cc_final: 0.8823 (t80) REVERT: A 213 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8457 (pp) REVERT: A 424 MET cc_start: 0.8861 (tpp) cc_final: 0.8470 (tmm) REVERT: A 449 MET cc_start: 0.7802 (ptp) cc_final: 0.6994 (ptm) REVERT: A 453 MET cc_start: 0.8473 (mtt) cc_final: 0.7921 (mtt) REVERT: A 638 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8102 (pp) REVERT: A 1011 MET cc_start: 0.8106 (mmp) cc_final: 0.7873 (mmt) REVERT: A 1181 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8774 (mm) outliers start: 9 outliers final: 3 residues processed: 46 average time/residue: 0.2145 time to fit residues: 15.9037 Evaluate side-chains 43 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 1053 ILE 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 62 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 53 optimal weight: 0.5980 chunk 59 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 100 optimal weight: 0.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 = 0.3556 r_free = 0.3556 target = 0.074873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.053916 restraints weight = 29016.130| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 3.23 r_work: 0.2923 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8580 Z= 0.303 Angle : 0.533 12.232 11647 Z= 0.269 Chirality : 0.041 0.180 1371 Planarity : 0.003 0.039 1478 Dihedral : 3.911 20.863 1167 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.82 % Allowed : 15.36 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.26), residues: 1080 helix: 2.01 (0.24), residues: 495 sheet: -1.94 (0.38), residues: 155 loop : -1.98 (0.25), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 218 HIS 0.006 0.001 HIS A 672 PHE 0.018 0.002 PHE A 226 TYR 0.009 0.001 TYR A1057 ARG 0.002 0.000 ARG A 260 *********************** 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 53 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 37 time to evaluate : 0.951 Fit side-chains revert: symmetry clash REVERT: A 207 PHE cc_start: 0.9181 (t80) cc_final: 0.8897 (t80) REVERT: A 213 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8443 (pp) REVERT: A 424 MET cc_start: 0.8797 (tpp) cc_final: 0.8430 (tmm) REVERT: A 449 MET cc_start: 0.7913 (ptp) cc_final: 0.6958 (ptm) REVERT: A 453 MET cc_start: 0.8571 (mtt) cc_final: 0.8050 (mtt) REVERT: A 1181 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8884 (mm) outliers start: 16 outliers final: 9 residues processed: 49 average time/residue: 0.1500 time to fit residues: 12.1958 Evaluate side-chains 46 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 1053 ILE 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 62 optimal weight: 8.9990 chunk 102 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 35 optimal weight: 0.8980 chunk 109 optimal weight: 50.0000 chunk 10 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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** ** A 566 ASN ** 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 = 0.3539 r_free = 0.3539 target = 0.074142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.053115 restraints weight = 28963.678| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 3.23 r_work: 0.2899 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8580 Z= 0.350 Angle : 0.572 11.406 11647 Z= 0.287 Chirality : 0.042 0.192 1371 Planarity : 0.003 0.040 1478 Dihedral : 4.113 21.321 1167 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.50 % Allowed : 15.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.26), residues: 1080 helix: 2.10 (0.24), residues: 489 sheet: -1.85 (0.39), residues: 152 loop : -1.98 (0.25), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1187 HIS 0.006 0.001 HIS A 672 PHE 0.020 0.002 PHE A 226 TYR 0.010 0.001 TYR A 625 ARG 0.004 0.000 ARG A 260 *********************** 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 59 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 37 time to evaluate : 0.975 Fit side-chains revert: symmetry clash REVERT: A 207 PHE cc_start: 0.9187 (t80) cc_final: 0.8936 (t80) REVERT: A 213 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8481 (pp) REVERT: A 449 MET cc_start: 0.7830 (ptp) cc_final: 0.7026 (ptm) REVERT: A 453 MET cc_start: 0.8679 (mtt) cc_final: 0.8200 (mtt) REVERT: A 638 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8208 (pp) REVERT: A 1136 MET cc_start: 0.6795 (tmm) cc_final: 0.6456 (tmm) REVERT: A 1181 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8883 (mm) outliers start: 22 outliers final: 13 residues processed: 55 average time/residue: 0.1387 time to fit residues: 12.9287 Evaluate side-chains 53 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 37 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 404 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 975 THR Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1114 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 23 optimal weight: 0.3980 chunk 30 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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** A1050 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.074551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.053977 restraints weight = 28905.669| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 3.20 r_work: 0.2919 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8580 Z= 0.273 Angle : 0.538 10.822 11647 Z= 0.267 Chirality : 0.041 0.177 1371 Planarity : 0.003 0.038 1478 Dihedral : 3.991 21.515 1167 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.16 % Allowed : 16.27 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.26), residues: 1080 helix: 2.17 (0.24), residues: 495 sheet: -1.69 (0.41), residues: 152 loop : -1.85 (0.26), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 418 HIS 0.006 0.001 HIS A 672 PHE 0.020 0.001 PHE A 226 TYR 0.009 0.001 TYR A 625 ARG 0.002 0.000 ARG A 260 *********************** 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 57 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 38 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: A 207 PHE cc_start: 0.9167 (t80) cc_final: 0.8912 (t80) REVERT: A 449 MET cc_start: 0.7817 (ptp) cc_final: 0.7006 (ptm) REVERT: A 453 MET cc_start: 0.8645 (mtt) cc_final: 0.8193 (mtt) REVERT: A 638 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8150 (pp) REVERT: A 1136 MET cc_start: 0.6871 (tmm) cc_final: 0.6498 (tmm) REVERT: A 1181 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8917 (mm) outliers start: 19 outliers final: 14 residues processed: 53 average time/residue: 0.1459 time to fit residues: 12.9853 Evaluate side-chains 53 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 37 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 489 THR 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 957 ASP Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1114 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 48 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 2 optimal weight: 20.0000 chunk 80 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 75 optimal weight: 0.0270 chunk 43 optimal weight: 9.9990 overall best weight: 2.2044 ------------------------------------------------------------------------------- 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** A1050 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.074536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.053541 restraints weight = 29184.775| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 3.25 r_work: 0.2909 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 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 : 0.004 0.044 8580 Z= 0.270 Angle : 0.543 10.526 11647 Z= 0.269 Chirality : 0.041 0.203 1371 Planarity : 0.003 0.038 1478 Dihedral : 3.984 21.399 1167 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.16 % Allowed : 16.61 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.26), residues: 1080 helix: 2.21 (0.24), residues: 495 sheet: -1.58 (0.41), residues: 152 loop : -1.82 (0.26), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 415 HIS 0.006 0.001 HIS A 672 PHE 0.020 0.001 PHE A 226 TYR 0.008 0.001 TYR A 761 ARG 0.002 0.000 ARG A 260 *********************** 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 56 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 37 time to evaluate : 0.908 Fit side-chains revert: symmetry clash REVERT: A 207 PHE cc_start: 0.9195 (t80) cc_final: 0.8961 (t80) REVERT: A 213 LEU cc_start: 0.9039 (tp) cc_final: 0.8580 (pp) REVERT: A 449 MET cc_start: 0.7793 (ptp) cc_final: 0.6990 (ptm) REVERT: A 453 MET cc_start: 0.8683 (mtt) cc_final: 0.8217 (mtt) REVERT: A 638 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8151 (pp) REVERT: A 1136 MET cc_start: 0.6859 (tmm) cc_final: 0.6459 (tmm) REVERT: A 1181 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8896 (mm) outliers start: 19 outliers final: 14 residues processed: 52 average time/residue: 0.1984 time to fit residues: 16.6995 Evaluate side-chains 53 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 37 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 404 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 975 THR Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1114 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 3 optimal weight: 10.0000 chunk 62 optimal weight: 0.0070 chunk 15 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 72 optimal weight: 0.4980 chunk 38 optimal weight: 0.9980 overall best weight: 0.9002 ------------------------------------------------------------------------------- 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 = 0.3572 r_free = 0.3572 target = 0.075595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.054475 restraints weight = 29278.073| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 3.45 r_work: 0.2931 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8580 Z= 0.145 Angle : 0.497 10.233 11647 Z= 0.243 Chirality : 0.039 0.212 1371 Planarity : 0.003 0.037 1478 Dihedral : 3.728 21.115 1167 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.59 % Allowed : 17.06 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.26), residues: 1080 helix: 2.44 (0.24), residues: 489 sheet: -1.41 (0.42), residues: 152 loop : -1.62 (0.26), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 418 HIS 0.006 0.001 HIS A 672 PHE 0.020 0.001 PHE A 226 TYR 0.006 0.001 TYR A 761 ARG 0.001 0.000 ARG A1048 *********************** 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 52 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 38 time to evaluate : 0.925 Fit side-chains revert: symmetry clash REVERT: A 207 PHE cc_start: 0.9131 (t80) cc_final: 0.8893 (t80) REVERT: A 213 LEU cc_start: 0.9080 (tp) cc_final: 0.8624 (pp) REVERT: A 227 MET cc_start: 0.7939 (ttp) cc_final: 0.7734 (ttt) REVERT: A 338 VAL cc_start: 0.9492 (OUTLIER) cc_final: 0.9156 (m) REVERT: A 449 MET cc_start: 0.7697 (ptp) cc_final: 0.6837 (ptm) REVERT: A 453 MET cc_start: 0.8682 (mtt) cc_final: 0.8171 (mtt) REVERT: A 638 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8033 (pp) REVERT: A 1136 MET cc_start: 0.6828 (tmm) cc_final: 0.6409 (tmm) REVERT: A 1181 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8826 (mm) outliers start: 14 outliers final: 7 residues processed: 49 average time/residue: 0.1409 time to fit residues: 12.0178 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 : 0.992 ------------------------------------------------------------------------------- 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 338 VAL Chi-restraints excluded: chain A residue 489 THR 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 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 34 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 13 optimal weight: 0.1980 chunk 36 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- 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 = 0.3569 r_free = 0.3569 target = 0.075114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.054182 restraints weight = 28885.301| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 3.42 r_work: 0.2914 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8580 Z= 0.208 Angle : 0.505 10.213 11647 Z= 0.249 Chirality : 0.040 0.211 1371 Planarity : 0.003 0.037 1478 Dihedral : 3.746 20.952 1167 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.48 % Allowed : 17.18 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.26), residues: 1080 helix: 2.45 (0.24), residues: 494 sheet: -1.38 (0.42), residues: 152 loop : -1.64 (0.26), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 415 HIS 0.006 0.001 HIS A 672 PHE 0.020 0.001 PHE A 226 TYR 0.007 0.001 TYR A 761 ARG 0.002 0.000 ARG A 260 ********************** 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 49 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: A 207 PHE cc_start: 0.9166 (t80) cc_final: 0.8936 (t80) REVERT: A 213 LEU cc_start: 0.9072 (tp) cc_final: 0.8688 (pp) REVERT: A 338 VAL cc_start: 0.9497 (OUTLIER) cc_final: 0.9162 (m) REVERT: A 449 MET cc_start: 0.7707 (ptp) cc_final: 0.6840 (ptm) REVERT: A 453 MET cc_start: 0.8674 (mtt) cc_final: 0.8166 (mtt) REVERT: A 638 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8090 (pp) REVERT: A 1136 MET cc_start: 0.6797 (tmm) cc_final: 0.6380 (tmm) REVERT: A 1181 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8844 (mm) outliers start: 13 outliers final: 10 residues processed: 46 average time/residue: 0.1498 time to fit residues: 11.3151 Evaluate side-chains 49 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 829 VAL 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 23 optimal weight: 0.0170 chunk 29 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 3 optimal weight: 30.0000 chunk 59 optimal weight: 2.9990 chunk 34 optimal weight: 0.0010 chunk 95 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.0026 ------------------------------------------------------------------------------- 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 = 0.3585 r_free = 0.3585 target = 0.075756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.054925 restraints weight = 29132.447| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.41 r_work: 0.2934 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8580 Z= 0.151 Angle : 0.500 10.146 11647 Z= 0.243 Chirality : 0.039 0.223 1371 Planarity : 0.003 0.037 1478 Dihedral : 3.650 20.871 1167 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.71 % Allowed : 16.95 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.26), residues: 1080 helix: 2.55 (0.24), residues: 490 sheet: -1.26 (0.42), residues: 153 loop : -1.45 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 787 HIS 0.006 0.001 HIS A 672 PHE 0.026 0.001 PHE A 226 TYR 0.006 0.001 TYR A 761 ARG 0.001 0.000 ARG A1127 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3795.41 seconds wall clock time: 67 minutes 52.16 seconds (4072.16 seconds total)