Starting phenix.real_space_refine on Tue Mar 3 17:06:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rd7_24414/03_2026/7rd7_24414.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rd7_24414/03_2026/7rd7_24414.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rd7_24414/03_2026/7rd7_24414.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rd7_24414/03_2026/7rd7_24414.map" model { file = "/net/cci-nas-00/data/ceres_data/7rd7_24414/03_2026/7rd7_24414.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rd7_24414/03_2026/7rd7_24414.cif" } resolution = 3.08 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= -0.000 sd= 0.003 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 Al 1 5.89 5 Mg 1 5.21 5 S 37 5.16 5 C 4762 2.51 5 N 1220 2.21 5 O 1375 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7400 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 929, 7394 Classifications: {'peptide': 929} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 902} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' MG': 1, 'ALF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.85, per 1000 atoms: 0.25 Number of scatterers: 7400 At special positions: 0 Unit cell: (74.34, 82.6, 140.42, 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 37 16.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1375 8.00 N 1220 7.00 C 4762 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 277.7 milliseconds 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1770 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 7 sheets defined 49.2% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 161 through 167 removed outlier: 4.054A pdb=" N TYR A 165 " --> pdb=" O THR A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 194 removed outlier: 3.571A pdb=" N LEU A 189 " --> pdb=" O PHE A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 209 removed outlier: 4.290A pdb=" N PHE A 202 " --> pdb=" O TYR A 198 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLN A 209 " --> pdb=" O VAL A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 250 Processing helix chain 'A' and resid 363 through 367 removed outlier: 3.564A pdb=" N THR A 367 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 396 removed outlier: 3.548A pdb=" N ASN A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 434 Processing helix chain 'A' and resid 439 through 452 Processing helix chain 'A' and resid 454 through 475 removed outlier: 3.745A pdb=" N SER A 458 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG A 460 " --> pdb=" O PRO A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 496 Processing helix chain 'A' and resid 530 through 538 Processing helix chain 'A' and resid 561 through 576 Processing helix chain 'A' and resid 594 through 608 removed outlier: 3.634A pdb=" N ILE A 598 " --> pdb=" O SER A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 671 Processing helix chain 'A' and resid 679 through 689 removed outlier: 3.666A pdb=" N GLU A 683 " --> pdb=" O TRP A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 712 removed outlier: 3.720A pdb=" N TYR A 707 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 766 Processing helix chain 'A' and resid 777 through 788 Processing helix chain 'A' and resid 827 through 838 Processing helix chain 'A' and resid 838 through 847 removed outlier: 3.639A pdb=" N PHE A 842 " --> pdb=" O TYR A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 873 Processing helix chain 'A' and resid 883 through 885 No H-bonds generated for 'chain 'A' and resid 883 through 885' Processing helix chain 'A' and resid 886 through 892 Processing helix chain 'A' and resid 905 through 911 removed outlier: 3.505A pdb=" N ALA A 910 " --> pdb=" O GLN A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 927 removed outlier: 4.421A pdb=" N GLU A 923 " --> pdb=" O CYS A 919 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TRP A 927 " --> pdb=" O GLU A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 961 Processing helix chain 'A' and resid 971 through 979 removed outlier: 3.861A pdb=" N VAL A 975 " --> pdb=" O GLY A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 990 removed outlier: 4.155A pdb=" N VAL A 986 " --> pdb=" O THR A 982 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE A 987 " --> pdb=" O MET A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1000 removed outlier: 3.527A pdb=" N THR A1000 " --> pdb=" O GLU A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1011 removed outlier: 3.862A pdb=" N LEU A1010 " --> pdb=" O TYR A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1044 Processing helix chain 'A' and resid 1049 through 1072 removed outlier: 3.517A pdb=" N ALA A1070 " --> pdb=" O LEU A1066 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU A1072 " --> pdb=" O MET A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1093 removed outlier: 3.882A pdb=" N ILE A1085 " --> pdb=" O LEU A1081 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR A1087 " --> pdb=" O THR A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1138 removed outlier: 3.895A pdb=" N SER A1123 " --> pdb=" O ILE A1119 " (cutoff:3.500A) Proline residue: A1126 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 155 through 157 removed outlier: 3.678A pdb=" N GLY A 350 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR A 354 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR A 358 " --> pdb=" O TYR A 354 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 255 through 257 Processing sheet with id=AA3, first strand: chain 'A' and resid 275 through 279 removed outlier: 7.573A pdb=" N PHE A 379 " --> pdb=" O SER A 293 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N SER A 293 " --> pdb=" O PHE A 379 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE A 381 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ASP A 287 " --> pdb=" O VAL A 385 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 299 through 303 Processing sheet with id=AA5, first strand: chain 'A' and resid 484 through 485 removed outlier: 6.785A pdb=" N GLY A 896 " --> pdb=" O PHE A 913 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE A 915 " --> pdb=" O GLY A 896 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N GLY A 898 " --> pdb=" O ILE A 915 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL A 877 " --> pdb=" O VAL A 895 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N VAL A 897 " --> pdb=" O VAL A 877 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N CYS A 879 " --> pdb=" O VAL A 897 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ILE A 899 " --> pdb=" O CYS A 879 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLY A 881 " --> pdb=" O ILE A 899 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU A 500 " --> pdb=" O TRP A 771 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N LEU A 773 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N SER A 502 " --> pdb=" O LEU A 773 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ILE A 770 " --> pdb=" O VAL A 852 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N ALA A 854 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N MET A 772 " --> pdb=" O ALA A 854 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 523 through 526 removed outlier: 6.311A pdb=" N MET A 513 " --> pdb=" O LYS A 751 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LYS A 751 " --> pdb=" O MET A 513 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LEU A 515 " --> pdb=" O GLU A 749 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N GLU A 749 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LEU A 742 " --> pdb=" O ARG A 699 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ARG A 699 " --> pdb=" O LEU A 742 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY A 744 " --> pdb=" O ILE A 697 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 748 " --> pdb=" O ARG A 693 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR A 659 " --> pdb=" O LEU A 702 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N GLY A 648 " --> pdb=" O VAL A 637 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL A 637 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE A 650 " --> pdb=" O LEU A 635 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HIS A 623 " --> pdb=" O LEU A 630 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU A 622 " --> pdb=" O PHE A 612 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 580 through 582 368 hydrogen bonds defined for protein. 1050 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: 1.38 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2340 1.34 - 1.46: 1548 1.46 - 1.58: 3592 1.58 - 1.70: 0 1.70 - 1.81: 61 Bond restraints: 7541 Sorted by residual: bond pdb=" F1 ALF A1201 " pdb="AL ALF A1201 " ideal model delta sigma weight residual 1.684 1.782 -0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" F3 ALF A1201 " pdb="AL ALF A1201 " ideal model delta sigma weight residual 1.685 1.782 -0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" F4 ALF A1201 " pdb="AL ALF A1201 " ideal model delta sigma weight residual 1.686 1.782 -0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" F2 ALF A1201 " pdb="AL ALF A1201 " ideal model delta sigma weight residual 1.685 1.778 -0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" N PRO A 285 " pdb=" CD PRO A 285 " ideal model delta sigma weight residual 1.473 1.443 0.030 1.40e-02 5.10e+03 4.49e+00 ... (remaining 7536 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.16: 10219 14.16 - 28.32: 4 28.32 - 42.49: 0 42.49 - 56.65: 0 56.65 - 70.81: 2 Bond angle restraints: 10225 Sorted by residual: angle pdb=" F1 ALF A1201 " pdb="AL ALF A1201 " pdb=" F2 ALF A1201 " ideal model delta sigma weight residual 108.68 179.49 -70.81 3.00e+00 1.11e-01 5.57e+02 angle pdb=" F3 ALF A1201 " pdb="AL ALF A1201 " pdb=" F4 ALF A1201 " ideal model delta sigma weight residual 109.63 178.84 -69.21 3.00e+00 1.11e-01 5.32e+02 angle pdb=" F2 ALF A1201 " pdb="AL ALF A1201 " pdb=" F4 ALF A1201 " ideal model delta sigma weight residual 110.21 89.14 21.07 3.00e+00 1.11e-01 4.93e+01 angle pdb=" F1 ALF A1201 " pdb="AL ALF A1201 " pdb=" F3 ALF A1201 " ideal model delta sigma weight residual 109.69 89.92 19.77 3.00e+00 1.11e-01 4.34e+01 angle pdb=" F2 ALF A1201 " pdb="AL ALF A1201 " pdb=" F3 ALF A1201 " ideal model delta sigma weight residual 109.59 90.28 19.31 3.00e+00 1.11e-01 4.14e+01 ... (remaining 10220 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 4104 17.74 - 35.47: 343 35.47 - 53.20: 58 53.20 - 70.94: 11 70.94 - 88.67: 9 Dihedral angle restraints: 4525 sinusoidal: 1792 harmonic: 2733 Sorted by residual: dihedral pdb=" CA TRP A 369 " pdb=" C TRP A 369 " pdb=" N ALA A 370 " pdb=" CA ALA A 370 " ideal model delta harmonic sigma weight residual -180.00 -156.96 -23.04 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA THR A 582 " pdb=" C THR A 582 " pdb=" N PHE A 583 " pdb=" CA PHE A 583 " ideal model delta harmonic sigma weight residual -180.00 -159.73 -20.27 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA THR A 979 " pdb=" C THR A 979 " pdb=" N CYS A 980 " pdb=" CA CYS A 980 " ideal model delta harmonic sigma weight residual -180.00 -160.52 -19.48 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 4522 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 751 0.039 - 0.077: 330 0.077 - 0.116: 104 0.116 - 0.155: 21 0.155 - 0.193: 5 Chirality restraints: 1211 Sorted by residual: chirality pdb=" CA GLU A 237 " pdb=" N GLU A 237 " pdb=" C GLU A 237 " pdb=" CB GLU A 237 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.34e-01 chirality pdb=" CB ILE A 334 " pdb=" CA ILE A 334 " pdb=" CG1 ILE A 334 " pdb=" CG2 ILE A 334 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.05e-01 chirality pdb=" CB VAL A 229 " pdb=" CA VAL A 229 " pdb=" CG1 VAL A 229 " pdb=" CG2 VAL A 229 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.00e-01 ... (remaining 1208 not shown) Planarity restraints: 1267 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 158 " 0.074 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO A 159 " -0.193 5.00e-02 4.00e+02 pdb=" CA PRO A 159 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 159 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 360 " -0.032 5.00e-02 4.00e+02 4.92e-02 3.87e+00 pdb=" N PRO A 361 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 361 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 361 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 858 " 0.031 5.00e-02 4.00e+02 4.74e-02 3.59e+00 pdb=" N PRO A 859 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 859 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 859 " 0.026 5.00e-02 4.00e+02 ... (remaining 1264 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 55 2.50 - 3.10: 5214 3.10 - 3.70: 11428 3.70 - 4.30: 16551 4.30 - 4.90: 27644 Nonbonded interactions: 60892 Sorted by model distance: nonbonded pdb=" O PHE A1102 " pdb=" OD1 ASP A1103 " model vdw 1.902 3.040 nonbonded pdb=" O ASP A 882 " pdb="MG MG A1202 " model vdw 2.128 2.170 nonbonded pdb=" OD1 ASN A 885 " pdb="MG MG A1202 " model vdw 2.130 2.170 nonbonded pdb=" O ASP A1100 " pdb=" OD1 ASP A1100 " model vdw 2.137 3.040 nonbonded pdb=" OG SER A 594 " pdb=" OD1 ASP A 596 " model vdw 2.241 3.040 ... (remaining 60887 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.720 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 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 : 0.005 0.098 7541 Z= 0.220 Angle : 1.331 70.809 10225 Z= 0.564 Chirality : 0.048 0.193 1211 Planarity : 0.005 0.112 1267 Dihedral : 13.974 88.675 2755 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.27), residues: 919 helix: -0.41 (0.24), residues: 419 sheet: -1.74 (0.42), residues: 150 loop : -1.72 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 567 TYR 0.025 0.002 TYR A 198 PHE 0.014 0.002 PHE A 843 TRP 0.018 0.002 TRP A 660 HIS 0.008 0.001 HIS A 945 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 7541) covalent geometry : angle 1.33101 (10225) hydrogen bonds : bond 0.13905 ( 368) hydrogen bonds : angle 6.34809 ( 1050) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.302 Fit side-chains REVERT: A 516 LYS cc_start: 0.8541 (ttmm) cc_final: 0.8193 (ttpp) REVERT: A 795 GLN cc_start: 0.8370 (tt0) cc_final: 0.7985 (tt0) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.0731 time to fit residues: 11.6647 Evaluate side-chains 92 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.0060 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 GLN A 945 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.186948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.151204 restraints weight = 7914.900| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 2.00 r_work: 0.3842 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3701 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7541 Z= 0.129 Angle : 0.891 31.335 10225 Z= 0.386 Chirality : 0.042 0.141 1211 Planarity : 0.005 0.070 1267 Dihedral : 4.995 22.768 1004 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.36 % Allowed : 8.20 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.28), residues: 919 helix: 0.06 (0.25), residues: 427 sheet: -1.64 (0.41), residues: 148 loop : -1.74 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 389 TYR 0.023 0.001 TYR A 707 PHE 0.034 0.001 PHE A 202 TRP 0.009 0.001 TRP A 369 HIS 0.007 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 7541) covalent geometry : angle 0.89138 (10225) hydrogen bonds : bond 0.03971 ( 368) hydrogen bonds : angle 4.92997 ( 1050) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 105 time to evaluate : 0.186 Fit side-chains REVERT: A 362 LEU cc_start: 0.6447 (mt) cc_final: 0.6044 (mt) REVERT: A 795 GLN cc_start: 0.8622 (tt0) cc_final: 0.8273 (tt0) REVERT: A 1079 THR cc_start: 0.7833 (t) cc_final: 0.7455 (m) outliers start: 3 outliers final: 3 residues processed: 107 average time/residue: 0.0699 time to fit residues: 10.8934 Evaluate side-chains 96 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 93 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain A residue 990 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 81 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 75 optimal weight: 0.3980 chunk 60 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 chunk 78 optimal weight: 0.0060 chunk 54 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 HIS ** A 360 ASN ** 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 = 0.4328 r_free = 0.4328 target = 0.188351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.155352 restraints weight = 7761.352| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 1.78 r_work: 0.3828 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3693 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7541 Z= 0.129 Angle : 0.879 31.548 10225 Z= 0.377 Chirality : 0.042 0.139 1211 Planarity : 0.004 0.049 1267 Dihedral : 4.818 23.195 1004 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 0.72 % Allowed : 10.86 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.28), residues: 919 helix: 0.28 (0.25), residues: 427 sheet: -1.55 (0.41), residues: 148 loop : -1.66 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 699 TYR 0.026 0.001 TYR A 707 PHE 0.024 0.001 PHE A 202 TRP 0.008 0.001 TRP A 369 HIS 0.006 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 7541) covalent geometry : angle 0.87899 (10225) hydrogen bonds : bond 0.03820 ( 368) hydrogen bonds : angle 4.69308 ( 1050) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 100 time to evaluate : 0.278 Fit side-chains revert: symmetry clash REVERT: A 795 GLN cc_start: 0.8572 (tt0) cc_final: 0.8225 (tt0) REVERT: A 1079 THR cc_start: 0.7833 (t) cc_final: 0.7470 (m) outliers start: 6 outliers final: 4 residues processed: 104 average time/residue: 0.0689 time to fit residues: 10.4986 Evaluate side-chains 96 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain A residue 708 GLU Chi-restraints excluded: chain A residue 990 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 90 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 60 optimal weight: 0.3980 chunk 7 optimal weight: 0.2980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.180276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.143829 restraints weight = 8073.988| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 2.02 r_work: 0.3752 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3612 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7541 Z= 0.184 Angle : 0.921 31.876 10225 Z= 0.402 Chirality : 0.044 0.143 1211 Planarity : 0.004 0.043 1267 Dihedral : 5.030 25.755 1004 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 1.57 % Allowed : 11.58 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.28), residues: 919 helix: 0.08 (0.25), residues: 429 sheet: -1.78 (0.39), residues: 156 loop : -1.57 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 316 TYR 0.023 0.002 TYR A1101 PHE 0.029 0.002 PHE A 202 TRP 0.007 0.001 TRP A 972 HIS 0.006 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 7541) covalent geometry : angle 0.92077 (10225) hydrogen bonds : bond 0.04375 ( 368) hydrogen bonds : angle 4.71798 ( 1050) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.275 Fit side-chains REVERT: A 223 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7537 (mp) REVERT: A 652 ARG cc_start: 0.6115 (ttp80) cc_final: 0.5868 (ttp80) REVERT: A 690 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7788 (mm-30) REVERT: A 795 GLN cc_start: 0.8648 (tt0) cc_final: 0.8385 (tt0) outliers start: 13 outliers final: 7 residues processed: 110 average time/residue: 0.0748 time to fit residues: 11.7982 Evaluate side-chains 99 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 990 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 29 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 69 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 891 GLN A 954 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.185092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.148959 restraints weight = 7926.302| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 2.03 r_work: 0.3805 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3664 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7541 Z= 0.123 Angle : 0.871 32.082 10225 Z= 0.372 Chirality : 0.042 0.164 1211 Planarity : 0.004 0.042 1267 Dihedral : 4.769 22.804 1004 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 1.69 % Allowed : 12.91 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.28), residues: 919 helix: 0.35 (0.25), residues: 429 sheet: -1.66 (0.40), residues: 155 loop : -1.60 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 699 TYR 0.019 0.001 TYR A 707 PHE 0.031 0.001 PHE A 202 TRP 0.009 0.001 TRP A 369 HIS 0.006 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 7541) covalent geometry : angle 0.87062 (10225) hydrogen bonds : bond 0.03737 ( 368) hydrogen bonds : angle 4.57783 ( 1050) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.271 Fit side-chains REVERT: A 223 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7452 (mp) REVERT: A 371 ASN cc_start: 0.8044 (m110) cc_final: 0.7841 (m110) REVERT: A 609 LEU cc_start: 0.8375 (tt) cc_final: 0.7959 (tp) REVERT: A 690 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7777 (mm-30) REVERT: A 795 GLN cc_start: 0.8620 (tt0) cc_final: 0.8328 (tt0) outliers start: 14 outliers final: 9 residues processed: 105 average time/residue: 0.0636 time to fit residues: 10.0507 Evaluate side-chains 98 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1069 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 40 optimal weight: 6.9990 chunk 66 optimal weight: 0.2980 chunk 4 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 1 optimal weight: 0.0010 chunk 12 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.185761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.149789 restraints weight = 7955.832| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 2.03 r_work: 0.3828 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3688 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7541 Z= 0.117 Angle : 0.864 31.998 10225 Z= 0.367 Chirality : 0.041 0.153 1211 Planarity : 0.004 0.042 1267 Dihedral : 4.679 22.532 1004 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 1.57 % Allowed : 13.63 % Favored : 84.80 % 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 are not related in a simple way. whole: -1.02 (0.28), residues: 919 helix: 0.45 (0.25), residues: 428 sheet: -1.61 (0.40), residues: 155 loop : -1.58 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 699 TYR 0.017 0.001 TYR A 707 PHE 0.031 0.001 PHE A 202 TRP 0.010 0.001 TRP A 369 HIS 0.005 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 7541) covalent geometry : angle 0.86371 (10225) hydrogen bonds : bond 0.03612 ( 368) hydrogen bonds : angle 4.54335 ( 1050) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.284 Fit side-chains REVERT: A 223 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7457 (mp) REVERT: A 371 ASN cc_start: 0.8011 (m110) cc_final: 0.7802 (m110) REVERT: A 568 ASP cc_start: 0.7792 (t0) cc_final: 0.7405 (t0) REVERT: A 609 LEU cc_start: 0.8425 (tt) cc_final: 0.8035 (tp) REVERT: A 662 MET cc_start: 0.6662 (mtt) cc_final: 0.6401 (mtt) REVERT: A 690 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7785 (mm-30) REVERT: A 795 GLN cc_start: 0.8612 (tt0) cc_final: 0.8325 (tt0) outliers start: 13 outliers final: 10 residues processed: 105 average time/residue: 0.0641 time to fit residues: 10.2277 Evaluate side-chains 102 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1069 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 42 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 12 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 0.3980 chunk 63 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.182655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.146815 restraints weight = 8054.148| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 1.97 r_work: 0.3793 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3652 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7541 Z= 0.148 Angle : 0.885 31.756 10225 Z= 0.380 Chirality : 0.043 0.154 1211 Planarity : 0.004 0.042 1267 Dihedral : 4.762 24.171 1004 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 1.93 % Allowed : 13.03 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.28), residues: 919 helix: 0.34 (0.25), residues: 428 sheet: -1.61 (0.40), residues: 155 loop : -1.52 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 389 TYR 0.015 0.001 TYR A 707 PHE 0.028 0.002 PHE A 202 TRP 0.007 0.001 TRP A 972 HIS 0.005 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 7541) covalent geometry : angle 0.88482 (10225) hydrogen bonds : bond 0.03959 ( 368) hydrogen bonds : angle 4.56909 ( 1050) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.278 Fit side-chains REVERT: A 223 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7587 (mp) REVERT: A 371 ASN cc_start: 0.8035 (m110) cc_final: 0.7820 (m110) REVERT: A 568 ASP cc_start: 0.7893 (t0) cc_final: 0.7456 (t0) REVERT: A 609 LEU cc_start: 0.8428 (tt) cc_final: 0.8089 (tp) REVERT: A 662 MET cc_start: 0.6835 (mtt) cc_final: 0.6552 (mtt) REVERT: A 690 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7842 (mm-30) REVERT: A 795 GLN cc_start: 0.8613 (tt0) cc_final: 0.8329 (tt0) REVERT: A 939 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7254 (tt) outliers start: 16 outliers final: 12 residues processed: 109 average time/residue: 0.0688 time to fit residues: 11.0833 Evaluate side-chains 104 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 923 GLU Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1069 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 85 optimal weight: 0.6980 chunk 43 optimal weight: 0.0000 chunk 83 optimal weight: 0.0870 chunk 35 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 4 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.4562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.187256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.151141 restraints weight = 8068.422| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 2.06 r_work: 0.3833 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3691 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7541 Z= 0.112 Angle : 0.857 32.064 10225 Z= 0.362 Chirality : 0.041 0.143 1211 Planarity : 0.003 0.042 1267 Dihedral : 4.558 21.323 1004 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 1.93 % Allowed : 13.39 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.28), residues: 919 helix: 0.55 (0.25), residues: 428 sheet: -1.50 (0.40), residues: 155 loop : -1.50 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 699 TYR 0.012 0.001 TYR A 165 PHE 0.033 0.001 PHE A 202 TRP 0.011 0.001 TRP A 369 HIS 0.004 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 7541) covalent geometry : angle 0.85701 (10225) hydrogen bonds : bond 0.03428 ( 368) hydrogen bonds : angle 4.44276 ( 1050) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.330 Fit side-chains REVERT: A 223 ILE cc_start: 0.7943 (OUTLIER) cc_final: 0.7425 (mp) REVERT: A 362 LEU cc_start: 0.6470 (mt) cc_final: 0.5989 (mt) REVERT: A 371 ASN cc_start: 0.7957 (m110) cc_final: 0.7718 (m110) REVERT: A 568 ASP cc_start: 0.7726 (t0) cc_final: 0.7371 (t0) REVERT: A 609 LEU cc_start: 0.8404 (tt) cc_final: 0.8075 (tp) REVERT: A 795 GLN cc_start: 0.8611 (tt0) cc_final: 0.8338 (tt0) outliers start: 16 outliers final: 10 residues processed: 109 average time/residue: 0.0672 time to fit residues: 10.8737 Evaluate side-chains 108 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 1069 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 2 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 49 optimal weight: 0.2980 chunk 28 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 46 optimal weight: 0.0570 chunk 43 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.186480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.150394 restraints weight = 7854.120| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 2.02 r_work: 0.3833 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3694 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7541 Z= 0.118 Angle : 0.867 31.847 10225 Z= 0.367 Chirality : 0.042 0.193 1211 Planarity : 0.003 0.043 1267 Dihedral : 4.534 21.850 1004 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 1.45 % Allowed : 14.11 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.28), residues: 919 helix: 0.55 (0.25), residues: 429 sheet: -1.50 (0.40), residues: 155 loop : -1.44 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 699 TYR 0.014 0.001 TYR A 707 PHE 0.032 0.001 PHE A 202 TRP 0.010 0.001 TRP A 369 HIS 0.005 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 7541) covalent geometry : angle 0.86695 (10225) hydrogen bonds : bond 0.03528 ( 368) hydrogen bonds : angle 4.44911 ( 1050) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.286 Fit side-chains REVERT: A 223 ILE cc_start: 0.7976 (OUTLIER) cc_final: 0.7453 (mp) REVERT: A 362 LEU cc_start: 0.6511 (mt) cc_final: 0.6033 (mt) REVERT: A 371 ASN cc_start: 0.7906 (m110) cc_final: 0.7705 (m110) REVERT: A 568 ASP cc_start: 0.7746 (t0) cc_final: 0.7344 (t0) REVERT: A 609 LEU cc_start: 0.8436 (tt) cc_final: 0.8102 (tp) REVERT: A 795 GLN cc_start: 0.8631 (tt0) cc_final: 0.8360 (tt0) REVERT: A 939 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.7151 (tt) outliers start: 12 outliers final: 10 residues processed: 105 average time/residue: 0.0664 time to fit residues: 10.2748 Evaluate side-chains 106 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1069 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 0.9980 chunk 87 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 20 optimal weight: 0.0670 chunk 35 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.186605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.150920 restraints weight = 7912.659| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 1.95 r_work: 0.3832 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3695 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7541 Z= 0.119 Angle : 0.866 31.812 10225 Z= 0.367 Chirality : 0.042 0.157 1211 Planarity : 0.003 0.043 1267 Dihedral : 4.526 21.900 1004 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 1.45 % Allowed : 14.35 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.28), residues: 919 helix: 0.57 (0.25), residues: 429 sheet: -1.49 (0.41), residues: 155 loop : -1.41 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 699 TYR 0.016 0.001 TYR A 707 PHE 0.031 0.001 PHE A 202 TRP 0.010 0.001 TRP A 369 HIS 0.005 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 7541) covalent geometry : angle 0.86593 (10225) hydrogen bonds : bond 0.03526 ( 368) hydrogen bonds : angle 4.43381 ( 1050) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: A 223 ILE cc_start: 0.8003 (OUTLIER) cc_final: 0.7478 (mp) REVERT: A 362 LEU cc_start: 0.6381 (mt) cc_final: 0.5958 (mt) REVERT: A 371 ASN cc_start: 0.7913 (m110) cc_final: 0.7705 (m110) REVERT: A 568 ASP cc_start: 0.7748 (t0) cc_final: 0.7381 (t0) REVERT: A 609 LEU cc_start: 0.8457 (tt) cc_final: 0.8136 (tp) REVERT: A 795 GLN cc_start: 0.8609 (tt0) cc_final: 0.8346 (tt0) REVERT: A 939 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7180 (tt) outliers start: 12 outliers final: 10 residues processed: 103 average time/residue: 0.0615 time to fit residues: 9.2118 Evaluate side-chains 105 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1069 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 86 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 51 optimal weight: 0.3980 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.184988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.148358 restraints weight = 7910.276| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 2.03 r_work: 0.3812 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3671 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7541 Z= 0.126 Angle : 0.871 31.750 10225 Z= 0.371 Chirality : 0.042 0.147 1211 Planarity : 0.003 0.042 1267 Dihedral : 4.541 22.716 1004 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 1.57 % Allowed : 14.60 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.28), residues: 919 helix: 0.55 (0.25), residues: 429 sheet: -1.50 (0.41), residues: 155 loop : -1.39 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 699 TYR 0.014 0.001 TYR A 707 PHE 0.031 0.002 PHE A 202 TRP 0.008 0.001 TRP A 369 HIS 0.004 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 7541) covalent geometry : angle 0.87053 (10225) hydrogen bonds : bond 0.03642 ( 368) hydrogen bonds : angle 4.44745 ( 1050) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2415.08 seconds wall clock time: 41 minutes 58.83 seconds (2518.83 seconds total)