Starting phenix.real_space_refine on Sun Dec 29 02:44:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q60_13848/12_2024/7q60_13848.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q60_13848/12_2024/7q60_13848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7q60_13848/12_2024/7q60_13848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q60_13848/12_2024/7q60_13848.map" model { file = "/net/cci-nas-00/data/ceres_data/7q60_13848/12_2024/7q60_13848.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q60_13848/12_2024/7q60_13848.cif" } resolution = 3.13 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= -0.001 sd= 0.012 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: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 6047 2.51 5 N 1554 2.21 5 O 1803 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9450 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1212, 9450 Classifications: {'peptide': 1212} Link IDs: {'PCIS': 1, 'PTRANS': 62, 'TRANS': 1148} Chain breaks: 4 Time building chain proxies: 6.07, per 1000 atoms: 0.64 Number of scatterers: 9450 At special positions: 0 Unit cell: (111.526, 87.2329, 126.985, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 46 16.00 O 1803 8.00 N 1554 7.00 C 6047 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 40 " - pdb=" SG CYS A 78 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 279 " distance=2.03 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 557 " distance=2.03 Simple disulfide: pdb=" SG CYS A 589 " - pdb=" SG CYS A 769 " distance=2.03 Simple disulfide: pdb=" SG CYS A 633 " - pdb=" SG CYS A 694 " distance=2.03 Simple disulfide: pdb=" SG CYS A 819 " - pdb=" SG CYS A 847 " distance=2.03 Simple disulfide: pdb=" SG CYS A 845 " - pdb=" SG CYS A 881 " distance=2.03 Simple disulfide: pdb=" SG CYS A 919 " - pdb=" SG CYS A1307 " distance=2.04 Simple disulfide: pdb=" SG CYS A1075 " - pdb=" SG CYS A1123 " distance=2.03 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: 2.41 Conformation dependent library (CDL) restraints added in 1.3 seconds 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2256 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 18 sheets defined 16.3% alpha, 34.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 176 through 178 No H-bonds generated for 'chain 'A' and resid 176 through 178' Processing helix chain 'A' and resid 596 through 602 removed outlier: 3.526A pdb=" N ARG A 602 " --> pdb=" O VAL A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 615 removed outlier: 3.757A pdb=" N MET A 615 " --> pdb=" O SER A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 677 Processing helix chain 'A' and resid 880 through 884 removed outlier: 3.957A pdb=" N GLY A 883 " --> pdb=" O PRO A 880 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN A 884 " --> pdb=" O CYS A 881 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 880 through 884' Processing helix chain 'A' and resid 956 through 962 removed outlier: 3.604A pdb=" N LEU A 960 " --> pdb=" O ALA A 956 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP A 961 " --> pdb=" O LEU A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 972 through 979 Processing helix chain 'A' and resid 979 through 990 removed outlier: 4.458A pdb=" N TYR A 983 " --> pdb=" O ALA A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1015 removed outlier: 3.848A pdb=" N GLN A1011 " --> pdb=" O GLU A1007 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS A1012 " --> pdb=" O ILE A1008 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N MET A1015 " --> pdb=" O GLN A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1047 Processing helix chain 'A' and resid 1056 through 1067 removed outlier: 3.547A pdb=" N GLN A1060 " --> pdb=" O PRO A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1102 Processing helix chain 'A' and resid 1103 through 1107 removed outlier: 3.789A pdb=" N LEU A1106 " --> pdb=" O ALA A1103 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU A1107 " --> pdb=" O ALA A1104 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1103 through 1107' Processing helix chain 'A' and resid 1115 through 1122 Processing helix chain 'A' and resid 1132 through 1146 removed outlier: 3.606A pdb=" N THR A1136 " --> pdb=" O THR A1132 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A1146 " --> pdb=" O TYR A1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1159 removed outlier: 3.620A pdb=" N GLN A1159 " --> pdb=" O LEU A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1192 through 1205 Processing helix chain 'A' and resid 1211 through 1227 Processing helix chain 'A' and resid 1240 through 1255 removed outlier: 3.731A pdb=" N ALA A1255 " --> pdb=" O TYR A1251 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 82 removed outlier: 7.992A pdb=" N LYS A 38 " --> pdb=" O PRO A 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 31 removed outlier: 6.591A pdb=" N LEU A 56 " --> pdb=" O LYS A 64 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N LYS A 64 " --> pdb=" O LEU A 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 121 through 126 Processing sheet with id=AA4, first strand: chain 'A' and resid 130 through 131 removed outlier: 4.346A pdb=" N THR A 205 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N SER A 156 " --> pdb=" O GLU A 173 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 219 through 223 Processing sheet with id=AA6, first strand: chain 'A' and resid 229 through 230 removed outlier: 6.671A pdb=" N LEU A 229 " --> pdb=" O SER A 336 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 341 through 346 removed outlier: 4.047A pdb=" N GLU A 345 " --> pdb=" O LYS A 360 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LYS A 360 " --> pdb=" O GLU A 345 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 350 through 351 removed outlier: 3.553A pdb=" N TYR A 351 " --> pdb=" O ARG A 443 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 456 removed outlier: 4.617A pdb=" N LEU A 471 " --> pdb=" O HIS A 456 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 499 through 507 removed outlier: 5.966A pdb=" N SER A 488 " --> pdb=" O ILE A 539 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ILE A 539 " --> pdb=" O SER A 488 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 563 through 567 Processing sheet with id=AB3, first strand: chain 'A' and resid 570 through 571 removed outlier: 3.512A pdb=" N GLN A 571 " --> pdb=" O THR A 785 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 736 through 738 removed outlier: 7.783A pdb=" N THR A 736 " --> pdb=" O ASP A 595 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ASP A 595 " --> pdb=" O THR A 736 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 738 " --> pdb=" O ALA A 593 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 729 through 730 removed outlier: 3.628A pdb=" N ILE A 898 " --> pdb=" O ARG A 730 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 729 through 730 removed outlier: 3.628A pdb=" N ILE A 898 " --> pdb=" O ARG A 730 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 790 through 795 Processing sheet with id=AB8, first strand: chain 'A' and resid 908 through 918 Processing sheet with id=AB9, first strand: chain 'A' and resid 925 through 930 392 hydrogen bonds defined for protein. 1089 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: 4.31 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3031 1.35 - 1.47: 2260 1.47 - 1.59: 4299 1.59 - 1.71: 4 1.71 - 1.83: 69 Bond restraints: 9663 Sorted by residual: bond pdb=" CG PRO A 133 " pdb=" CD PRO A 133 " ideal model delta sigma weight residual 1.503 1.304 0.199 3.40e-02 8.65e+02 3.42e+01 bond pdb=" CB PRO A 133 " pdb=" CG PRO A 133 " ideal model delta sigma weight residual 1.492 1.662 -0.170 5.00e-02 4.00e+02 1.16e+01 bond pdb=" CB PRO A 400 " pdb=" CG PRO A 400 " ideal model delta sigma weight residual 1.492 1.660 -0.168 5.00e-02 4.00e+02 1.13e+01 bond pdb=" N PRO A 133 " pdb=" CD PRO A 133 " ideal model delta sigma weight residual 1.473 1.519 -0.046 1.40e-02 5.10e+03 1.09e+01 bond pdb=" CB PRO A 461 " pdb=" CG PRO A 461 " ideal model delta sigma weight residual 1.492 1.634 -0.142 5.00e-02 4.00e+02 8.03e+00 ... (remaining 9658 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.00: 12992 5.00 - 10.01: 110 10.01 - 15.01: 26 15.01 - 20.02: 1 20.02 - 25.02: 1 Bond angle restraints: 13130 Sorted by residual: angle pdb=" CA PRO A 133 " pdb=" N PRO A 133 " pdb=" CD PRO A 133 " ideal model delta sigma weight residual 112.00 93.89 18.11 1.40e+00 5.10e-01 1.67e+02 angle pdb=" CB MET A 966 " pdb=" CG MET A 966 " pdb=" SD MET A 966 " ideal model delta sigma weight residual 112.70 137.72 -25.02 3.00e+00 1.11e-01 6.96e+01 angle pdb=" N PRO A 133 " pdb=" CD PRO A 133 " pdb=" CG PRO A 133 " ideal model delta sigma weight residual 103.20 90.93 12.27 1.50e+00 4.44e-01 6.70e+01 angle pdb=" CA PRO A 400 " pdb=" N PRO A 400 " pdb=" CD PRO A 400 " ideal model delta sigma weight residual 112.00 102.86 9.14 1.40e+00 5.10e-01 4.26e+01 angle pdb=" C VAL A1112 " pdb=" N ASP A1113 " pdb=" CA ASP A1113 " ideal model delta sigma weight residual 124.82 136.32 -11.50 1.78e+00 3.16e-01 4.17e+01 ... (remaining 13125 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 5111 17.94 - 35.87: 536 35.87 - 53.81: 124 53.81 - 71.74: 25 71.74 - 89.68: 8 Dihedral angle restraints: 5804 sinusoidal: 2289 harmonic: 3515 Sorted by residual: dihedral pdb=" CB CYS A 919 " pdb=" SG CYS A 919 " pdb=" SG CYS A1307 " pdb=" CB CYS A1307 " ideal model delta sinusoidal sigma weight residual -86.00 -5.22 -80.78 1 1.00e+01 1.00e-02 8.06e+01 dihedral pdb=" CA PHE A 616 " pdb=" C PHE A 616 " pdb=" N PRO A 617 " pdb=" CA PRO A 617 " ideal model delta harmonic sigma weight residual -180.00 -141.02 -38.98 0 5.00e+00 4.00e-02 6.08e+01 dihedral pdb=" CA PRO A1320 " pdb=" C PRO A1320 " pdb=" N PRO A1321 " pdb=" CA PRO A1321 " ideal model delta harmonic sigma weight residual 180.00 146.08 33.92 0 5.00e+00 4.00e-02 4.60e+01 ... (remaining 5801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1276 0.086 - 0.171: 168 0.171 - 0.257: 35 0.257 - 0.343: 5 0.343 - 0.428: 4 Chirality restraints: 1488 Sorted by residual: chirality pdb=" CG LEU A 601 " pdb=" CB LEU A 601 " pdb=" CD1 LEU A 601 " pdb=" CD2 LEU A 601 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.59e+00 chirality pdb=" CB VAL A 627 " pdb=" CA VAL A 627 " pdb=" CG1 VAL A 627 " pdb=" CG2 VAL A 627 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" CB ILE A 96 " pdb=" CA ILE A 96 " pdb=" CG1 ILE A 96 " pdb=" CG2 ILE A 96 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.25e+00 ... (remaining 1485 not shown) Planarity restraints: 1690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 132 " -0.129 5.00e-02 4.00e+02 1.76e-01 4.96e+01 pdb=" N PRO A 133 " 0.303 5.00e-02 4.00e+02 pdb=" CA PRO A 133 " -0.092 5.00e-02 4.00e+02 pdb=" CD PRO A 133 " -0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A1320 " 0.083 5.00e-02 4.00e+02 1.23e-01 2.43e+01 pdb=" N PRO A1321 " -0.213 5.00e-02 4.00e+02 pdb=" CA PRO A1321 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO A1321 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 460 " -0.073 5.00e-02 4.00e+02 1.05e-01 1.76e+01 pdb=" N PRO A 461 " 0.181 5.00e-02 4.00e+02 pdb=" CA PRO A 461 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 461 " -0.056 5.00e-02 4.00e+02 ... (remaining 1687 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2272 2.80 - 3.32: 7503 3.32 - 3.85: 15923 3.85 - 4.37: 17115 4.37 - 4.90: 30864 Nonbonded interactions: 73677 Sorted by model distance: nonbonded pdb=" OG1 THR A 58 " pdb=" OE2 GLU A 92 " model vdw 2.271 3.040 nonbonded pdb=" OG SER A1145 " pdb=" OG1 THR A1206 " model vdw 2.319 3.040 nonbonded pdb=" OG1 THR A 143 " pdb=" OH TYR A 155 " model vdw 2.324 3.040 nonbonded pdb=" O ALA A 827 " pdb=" OH TYR A 832 " model vdw 2.332 3.040 nonbonded pdb=" OD1 ASN A 22 " pdb=" OG SER A 44 " model vdw 2.333 3.040 ... (remaining 73672 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: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.400 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 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 : 0.007 0.199 9663 Z= 0.393 Angle : 1.264 25.022 13130 Z= 0.652 Chirality : 0.066 0.428 1488 Planarity : 0.011 0.176 1690 Dihedral : 15.638 89.678 3518 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.16 % Favored : 94.76 % Rotamer: Outliers : 0.57 % Allowed : 17.70 % Favored : 81.73 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 0.09 % 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: -2.64 (0.22), residues: 1202 helix: -3.24 (0.24), residues: 192 sheet: -0.26 (0.23), residues: 498 loop : -2.66 (0.23), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A1173 HIS 0.007 0.001 HIS A 366 PHE 0.052 0.004 PHE A1286 TYR 0.046 0.003 TYR A 537 ARG 0.023 0.001 ARG A 602 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 109 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 540 PHE cc_start: 0.8241 (m-10) cc_final: 0.8037 (m-10) REVERT: A 555 GLU cc_start: 0.8044 (pp20) cc_final: 0.7483 (tp30) REVERT: A 766 MET cc_start: 0.8157 (tmm) cc_final: 0.7777 (ppp) outliers start: 6 outliers final: 3 residues processed: 114 average time/residue: 0.2076 time to fit residues: 34.4816 Evaluate side-chains 109 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 106 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 1136 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 109 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS A 161 GLN ** A1137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1154 ASN A1277 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 9663 Z= 0.222 Angle : 0.635 9.464 13130 Z= 0.321 Chirality : 0.043 0.215 1488 Planarity : 0.006 0.082 1690 Dihedral : 5.344 33.826 1296 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.83 % Favored : 95.09 % Rotamer: Outliers : 3.24 % Allowed : 16.75 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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: -1.94 (0.23), residues: 1202 helix: -1.62 (0.33), residues: 202 sheet: -0.19 (0.24), residues: 494 loop : -2.23 (0.25), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1173 HIS 0.002 0.001 HIS A1018 PHE 0.031 0.002 PHE A1286 TYR 0.015 0.001 TYR A 945 ARG 0.005 0.000 ARG A1274 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 110 time to evaluate : 1.121 Fit side-chains revert: symmetry clash REVERT: A 555 GLU cc_start: 0.7910 (pp20) cc_final: 0.7573 (pp20) REVERT: A 766 MET cc_start: 0.8327 (tmm) cc_final: 0.8027 (ppp) REVERT: A 966 MET cc_start: 0.7116 (ppp) cc_final: 0.6914 (ppp) REVERT: A 1066 MET cc_start: 0.6261 (pmm) cc_final: 0.5698 (mpp) REVERT: A 1108 MET cc_start: 0.4752 (mpp) cc_final: 0.4551 (mpp) outliers start: 34 outliers final: 19 residues processed: 133 average time/residue: 0.1953 time to fit residues: 38.8272 Evaluate side-chains 116 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1199 TYR Chi-restraints excluded: chain A residue 1235 PHE Chi-restraints excluded: chain A residue 1312 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 74 optimal weight: 0.0570 chunk 30 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 118 optimal weight: 0.0570 chunk 98 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN A 854 HIS ** A1137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1159 GLN A1204 GLN A1277 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9663 Z= 0.224 Angle : 0.612 8.598 13130 Z= 0.308 Chirality : 0.043 0.171 1488 Planarity : 0.005 0.055 1690 Dihedral : 4.953 30.997 1294 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.74 % Favored : 95.17 % Rotamer: Outliers : 4.09 % Allowed : 17.22 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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: -1.58 (0.24), residues: 1202 helix: -0.80 (0.36), residues: 201 sheet: -0.17 (0.23), residues: 499 loop : -2.03 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1173 HIS 0.002 0.001 HIS A 914 PHE 0.024 0.002 PHE A1286 TYR 0.020 0.001 TYR A1135 ARG 0.005 0.000 ARG A1274 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 100 time to evaluate : 1.348 Fit side-chains revert: symmetry clash REVERT: A 522 LEU cc_start: 0.6812 (OUTLIER) cc_final: 0.6449 (mm) REVERT: A 536 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8672 (mp) REVERT: A 555 GLU cc_start: 0.7819 (pp20) cc_final: 0.7312 (pp20) REVERT: A 601 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8597 (mm) REVERT: A 610 ARG cc_start: 0.7750 (tpm170) cc_final: 0.7464 (tpm170) REVERT: A 766 MET cc_start: 0.7997 (tmm) cc_final: 0.7683 (ppp) REVERT: A 977 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7066 (pp) REVERT: A 1066 MET cc_start: 0.6014 (OUTLIER) cc_final: 0.5736 (mpp) REVERT: A 1215 ILE cc_start: 0.5384 (OUTLIER) cc_final: 0.4643 (mt) REVERT: A 1272 PHE cc_start: 0.7986 (t80) cc_final: 0.7710 (t80) REVERT: A 1274 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.8008 (tpt90) outliers start: 43 outliers final: 25 residues processed: 130 average time/residue: 0.2043 time to fit residues: 39.0407 Evaluate side-chains 125 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1066 MET Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1199 TYR Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1235 PHE Chi-restraints excluded: chain A residue 1274 ARG Chi-restraints excluded: chain A residue 1312 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1159 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9663 Z= 0.211 Angle : 0.601 13.967 13130 Z= 0.301 Chirality : 0.043 0.195 1488 Planarity : 0.004 0.043 1690 Dihedral : 4.829 29.807 1294 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.24 % Favored : 94.68 % Rotamer: Outliers : 4.28 % Allowed : 17.22 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -1.35 (0.24), residues: 1202 helix: -0.45 (0.38), residues: 198 sheet: -0.11 (0.23), residues: 499 loop : -1.85 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1173 HIS 0.002 0.001 HIS A 914 PHE 0.031 0.001 PHE A1286 TYR 0.016 0.001 TYR A 732 ARG 0.004 0.000 ARG A1274 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 97 time to evaluate : 1.043 Fit side-chains REVERT: A 522 LEU cc_start: 0.6818 (OUTLIER) cc_final: 0.6424 (mm) REVERT: A 536 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8575 (mp) REVERT: A 601 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8579 (mm) REVERT: A 733 PHE cc_start: 0.6899 (OUTLIER) cc_final: 0.5769 (p90) REVERT: A 977 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7232 (pp) REVERT: A 1049 GLN cc_start: 0.5361 (OUTLIER) cc_final: 0.5017 (pp30) REVERT: A 1066 MET cc_start: 0.6017 (OUTLIER) cc_final: 0.5618 (mpp) REVERT: A 1215 ILE cc_start: 0.5408 (OUTLIER) cc_final: 0.4659 (mt) REVERT: A 1272 PHE cc_start: 0.7967 (t80) cc_final: 0.7650 (t80) outliers start: 45 outliers final: 25 residues processed: 129 average time/residue: 0.1842 time to fit residues: 35.3503 Evaluate side-chains 122 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 89 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1049 GLN Chi-restraints excluded: chain A residue 1066 MET Chi-restraints excluded: chain A residue 1199 TYR Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1235 PHE Chi-restraints excluded: chain A residue 1312 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 87 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 ASN ** A1137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9663 Z= 0.203 Angle : 0.595 13.904 13130 Z= 0.297 Chirality : 0.043 0.188 1488 Planarity : 0.004 0.041 1690 Dihedral : 4.706 29.618 1294 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.83 % Favored : 95.09 % Rotamer: Outliers : 4.09 % Allowed : 16.94 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -1.20 (0.24), residues: 1202 helix: -0.25 (0.38), residues: 198 sheet: -0.04 (0.23), residues: 498 loop : -1.75 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1173 HIS 0.002 0.000 HIS A 914 PHE 0.024 0.001 PHE A1286 TYR 0.012 0.001 TYR A1135 ARG 0.005 0.000 ARG A1274 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 98 time to evaluate : 1.104 Fit side-chains REVERT: A 162 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7348 (m-30) REVERT: A 342 MET cc_start: 0.6523 (OUTLIER) cc_final: 0.6284 (ppp) REVERT: A 501 MET cc_start: 0.8217 (ttp) cc_final: 0.7954 (ttt) REVERT: A 522 LEU cc_start: 0.6882 (OUTLIER) cc_final: 0.6537 (mm) REVERT: A 536 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8546 (mp) REVERT: A 537 TYR cc_start: 0.8483 (p90) cc_final: 0.8249 (p90) REVERT: A 601 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8586 (mm) REVERT: A 610 ARG cc_start: 0.7664 (tpm170) cc_final: 0.7341 (tpm170) REVERT: A 733 PHE cc_start: 0.6998 (OUTLIER) cc_final: 0.5940 (p90) REVERT: A 977 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7341 (pp) REVERT: A 1049 GLN cc_start: 0.5063 (OUTLIER) cc_final: 0.4738 (pp30) REVERT: A 1066 MET cc_start: 0.6086 (OUTLIER) cc_final: 0.5461 (mpp) REVERT: A 1215 ILE cc_start: 0.5402 (OUTLIER) cc_final: 0.4656 (mt) outliers start: 43 outliers final: 27 residues processed: 129 average time/residue: 0.1875 time to fit residues: 35.9451 Evaluate side-chains 126 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 89 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1049 GLN Chi-restraints excluded: chain A residue 1066 MET Chi-restraints excluded: chain A residue 1113 ASP Chi-restraints excluded: chain A residue 1199 TYR Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1235 PHE Chi-restraints excluded: chain A residue 1312 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 97 optimal weight: 0.0770 chunk 54 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 112 optimal weight: 5.9990 overall best weight: 1.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 986 GLN ** A1137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1277 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 9663 Z= 0.356 Angle : 0.682 17.196 13130 Z= 0.342 Chirality : 0.045 0.202 1488 Planarity : 0.004 0.043 1690 Dihedral : 5.154 31.335 1294 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.07 % Favored : 93.84 % Rotamer: Outliers : 4.38 % Allowed : 17.79 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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: -1.40 (0.24), residues: 1202 helix: -0.46 (0.36), residues: 198 sheet: -0.20 (0.23), residues: 497 loop : -1.82 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A1173 HIS 0.004 0.001 HIS A 914 PHE 0.036 0.002 PHE A1286 TYR 0.015 0.002 TYR A1135 ARG 0.005 0.000 ARG A1274 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 100 time to evaluate : 1.079 Fit side-chains REVERT: A 144 MET cc_start: 0.8403 (mmt) cc_final: 0.7638 (mmt) REVERT: A 162 ASP cc_start: 0.8225 (OUTLIER) cc_final: 0.7531 (m-30) REVERT: A 342 MET cc_start: 0.6275 (OUTLIER) cc_final: 0.6058 (ppp) REVERT: A 501 MET cc_start: 0.8132 (ttp) cc_final: 0.7822 (ttt) REVERT: A 536 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8623 (mt) REVERT: A 537 TYR cc_start: 0.8410 (p90) cc_final: 0.8160 (p90) REVERT: A 601 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8793 (mm) REVERT: A 733 PHE cc_start: 0.7463 (OUTLIER) cc_final: 0.7021 (p90) REVERT: A 977 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7325 (pp) outliers start: 46 outliers final: 29 residues processed: 134 average time/residue: 0.1824 time to fit residues: 36.7728 Evaluate side-chains 131 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 96 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1113 ASP Chi-restraints excluded: chain A residue 1171 ILE Chi-restraints excluded: chain A residue 1199 TYR Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1235 PHE Chi-restraints excluded: chain A residue 1312 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 986 GLN A1277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9663 Z= 0.199 Angle : 0.632 15.794 13130 Z= 0.312 Chirality : 0.044 0.197 1488 Planarity : 0.004 0.045 1690 Dihedral : 4.848 29.865 1294 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.91 % Favored : 95.01 % Rotamer: Outliers : 3.81 % Allowed : 18.27 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -1.18 (0.24), residues: 1202 helix: -0.18 (0.38), residues: 197 sheet: -0.07 (0.23), residues: 495 loop : -1.72 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1173 HIS 0.002 0.000 HIS A 914 PHE 0.026 0.002 PHE A 33 TYR 0.013 0.001 TYR A 732 ARG 0.003 0.000 ARG A1274 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 103 time to evaluate : 1.103 Fit side-chains REVERT: A 144 MET cc_start: 0.8329 (mmt) cc_final: 0.7932 (mmt) REVERT: A 162 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7447 (m-30) REVERT: A 342 MET cc_start: 0.6524 (OUTLIER) cc_final: 0.6274 (ppp) REVERT: A 536 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8601 (mt) REVERT: A 537 TYR cc_start: 0.8479 (p90) cc_final: 0.8267 (p90) REVERT: A 601 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8690 (mm) REVERT: A 610 ARG cc_start: 0.7602 (tpm170) cc_final: 0.7332 (tpm170) REVERT: A 732 TYR cc_start: 0.6703 (p90) cc_final: 0.6389 (p90) REVERT: A 977 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.7060 (pp) REVERT: A 1215 ILE cc_start: 0.5553 (OUTLIER) cc_final: 0.4816 (mt) REVERT: A 1288 GLN cc_start: 0.8418 (pp30) cc_final: 0.7891 (pp30) outliers start: 40 outliers final: 26 residues processed: 134 average time/residue: 0.1996 time to fit residues: 41.2200 Evaluate side-chains 128 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 96 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1113 ASP Chi-restraints excluded: chain A residue 1199 TYR Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1235 PHE Chi-restraints excluded: chain A residue 1287 GLN Chi-restraints excluded: chain A residue 1312 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 79 optimal weight: 9.9990 chunk 57 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 986 GLN ** A1137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9663 Z= 0.250 Angle : 0.656 18.319 13130 Z= 0.322 Chirality : 0.044 0.196 1488 Planarity : 0.004 0.045 1690 Dihedral : 4.868 29.805 1294 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.16 % Favored : 93.76 % Rotamer: Outliers : 3.81 % Allowed : 18.74 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -1.18 (0.24), residues: 1202 helix: -0.04 (0.38), residues: 192 sheet: -0.11 (0.23), residues: 495 loop : -1.70 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1173 HIS 0.002 0.000 HIS A 914 PHE 0.035 0.002 PHE A1286 TYR 0.014 0.001 TYR A 732 ARG 0.003 0.000 ARG A1274 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 97 time to evaluate : 0.971 Fit side-chains REVERT: A 144 MET cc_start: 0.8418 (mmt) cc_final: 0.8011 (mmt) REVERT: A 342 MET cc_start: 0.6558 (OUTLIER) cc_final: 0.6313 (ppp) REVERT: A 536 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8620 (mt) REVERT: A 537 TYR cc_start: 0.8484 (p90) cc_final: 0.8260 (p90) REVERT: A 601 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8718 (mm) REVERT: A 610 ARG cc_start: 0.7617 (tpm170) cc_final: 0.7305 (tpm170) REVERT: A 977 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.6974 (pp) REVERT: A 1215 ILE cc_start: 0.5547 (OUTLIER) cc_final: 0.4812 (mt) REVERT: A 1288 GLN cc_start: 0.8453 (pp30) cc_final: 0.7903 (pp30) outliers start: 40 outliers final: 29 residues processed: 129 average time/residue: 0.1881 time to fit residues: 36.5127 Evaluate side-chains 130 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 96 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1113 ASP Chi-restraints excluded: chain A residue 1199 TYR Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1235 PHE Chi-restraints excluded: chain A residue 1287 GLN Chi-restraints excluded: chain A residue 1307 CYS Chi-restraints excluded: chain A residue 1312 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 1.9990 chunk 65 optimal weight: 0.0050 chunk 47 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 98 optimal weight: 0.0170 chunk 102 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.7836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9663 Z= 0.208 Angle : 0.645 15.334 13130 Z= 0.315 Chirality : 0.044 0.191 1488 Planarity : 0.004 0.046 1690 Dihedral : 4.757 29.207 1294 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.24 % Favored : 94.68 % Rotamer: Outliers : 3.81 % Allowed : 18.84 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -1.08 (0.24), residues: 1202 helix: 0.13 (0.38), residues: 190 sheet: -0.07 (0.23), residues: 495 loop : -1.64 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1173 HIS 0.002 0.000 HIS A 914 PHE 0.022 0.001 PHE A 33 TYR 0.014 0.001 TYR A1142 ARG 0.003 0.000 ARG A 602 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 98 time to evaluate : 1.107 Fit side-chains REVERT: A 177 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7653 (pm20) REVERT: A 342 MET cc_start: 0.6562 (OUTLIER) cc_final: 0.6308 (ppp) REVERT: A 536 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8654 (mt) REVERT: A 601 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8617 (mm) REVERT: A 732 TYR cc_start: 0.6698 (p90) cc_final: 0.6473 (p90) REVERT: A 977 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.6955 (pp) REVERT: A 1215 ILE cc_start: 0.5468 (OUTLIER) cc_final: 0.4728 (mt) REVERT: A 1288 GLN cc_start: 0.8450 (pp30) cc_final: 0.7916 (pp30) outliers start: 40 outliers final: 28 residues processed: 130 average time/residue: 0.1853 time to fit residues: 36.0433 Evaluate side-chains 126 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 92 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1113 ASP Chi-restraints excluded: chain A residue 1199 TYR Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1235 PHE Chi-restraints excluded: chain A residue 1287 GLN Chi-restraints excluded: chain A residue 1307 CYS Chi-restraints excluded: chain A residue 1312 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 58 optimal weight: 0.2980 chunk 76 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9663 Z= 0.251 Angle : 0.685 19.500 13130 Z= 0.331 Chirality : 0.044 0.212 1488 Planarity : 0.004 0.047 1690 Dihedral : 4.833 29.253 1294 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.07 % Favored : 93.84 % Rotamer: Outliers : 3.43 % Allowed : 19.51 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -1.14 (0.24), residues: 1202 helix: 0.11 (0.38), residues: 190 sheet: -0.17 (0.23), residues: 495 loop : -1.64 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1173 HIS 0.002 0.000 HIS A 77 PHE 0.035 0.002 PHE A1286 TYR 0.022 0.001 TYR A 537 ARG 0.003 0.000 ARG A1274 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 93 time to evaluate : 1.095 Fit side-chains REVERT: A 60 ASP cc_start: 0.8366 (p0) cc_final: 0.7792 (p0) REVERT: A 162 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7603 (m-30) REVERT: A 177 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7712 (pm20) REVERT: A 342 MET cc_start: 0.6579 (OUTLIER) cc_final: 0.6337 (ppp) REVERT: A 536 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8656 (mp) REVERT: A 601 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8508 (mm) REVERT: A 610 ARG cc_start: 0.7599 (tpm170) cc_final: 0.7382 (tpm170) REVERT: A 732 TYR cc_start: 0.6841 (p90) cc_final: 0.6536 (p90) REVERT: A 977 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7032 (pp) REVERT: A 1215 ILE cc_start: 0.5518 (OUTLIER) cc_final: 0.4785 (mt) REVERT: A 1288 GLN cc_start: 0.8488 (pp30) cc_final: 0.7927 (pp30) outliers start: 36 outliers final: 29 residues processed: 121 average time/residue: 0.1864 time to fit residues: 33.9173 Evaluate side-chains 128 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 92 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1113 ASP Chi-restraints excluded: chain A residue 1199 TYR Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1235 PHE Chi-restraints excluded: chain A residue 1287 GLN Chi-restraints excluded: chain A residue 1307 CYS Chi-restraints excluded: chain A residue 1312 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 40 optimal weight: 0.2980 chunk 98 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 84 optimal weight: 0.0030 chunk 5 optimal weight: 0.0060 chunk 69 optimal weight: 0.6980 overall best weight: 0.2806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 ASN A1277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.147740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.116653 restraints weight = 21543.698| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 4.57 r_work: 0.3674 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9663 Z= 0.170 Angle : 0.656 17.948 13130 Z= 0.315 Chirality : 0.044 0.213 1488 Planarity : 0.004 0.047 1690 Dihedral : 4.563 27.285 1294 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.58 % Favored : 95.34 % Rotamer: Outliers : 3.04 % Allowed : 19.98 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -0.94 (0.24), residues: 1202 helix: 0.36 (0.39), residues: 190 sheet: 0.08 (0.24), residues: 472 loop : -1.63 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1173 HIS 0.002 0.000 HIS A 830 PHE 0.016 0.001 PHE A1286 TYR 0.017 0.001 TYR A 537 ARG 0.002 0.000 ARG A 602 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2109.10 seconds wall clock time: 39 minutes 26.77 seconds (2366.77 seconds total)