Starting phenix.real_space_refine on Sun Jul 27 19:24:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q60_13848/07_2025/7q60_13848.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q60_13848/07_2025/7q60_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_13848/07_2025/7q60_13848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q60_13848/07_2025/7q60_13848.map" model { file = "/net/cci-nas-00/data/ceres_data/7q60_13848/07_2025/7q60_13848.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q60_13848/07_2025/7q60_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 5.74, per 1000 atoms: 0.61 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: 2.19 Conformation dependent library (CDL) restraints added in 1.1 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: 1.33 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: 3.97 Time building geometry restraints manager: 2.63 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: 1.720 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.230 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.530 ------------------------------------------------------------------------------- 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 9673 Z= 0.286 Angle : 1.265 25.022 13150 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 Details of bonding type rmsd hydrogen bonds : bond 0.10887 ( 383) hydrogen bonds : angle 7.03483 ( 1089) SS BOND : bond 0.00338 ( 10) SS BOND : angle 1.38223 ( 20) covalent geometry : bond 0.00673 ( 9663) covalent geometry : angle 1.26432 (13130) *********************** 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 : 1.081 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: 0.2001 time to fit residues: 33.2488 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 : 1.050 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.148722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.115978 restraints weight = 21597.142| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 4.48 r_work: 0.3720 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 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 9673 Z= 0.151 Angle : 0.636 9.464 13150 Z= 0.322 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 Details of bonding type rmsd hydrogen bonds : bond 0.03443 ( 383) hydrogen bonds : angle 5.73085 ( 1089) SS BOND : bond 0.00172 ( 10) SS BOND : angle 0.88523 ( 20) covalent geometry : bond 0.00352 ( 9663) covalent geometry : angle 0.63545 (13130) *********************** 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 : 0.984 Fit side-chains revert: symmetry clash REVERT: A 555 GLU cc_start: 0.7916 (pp20) cc_final: 0.7578 (pp20) REVERT: A 731 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7798 (pm20) REVERT: A 766 MET cc_start: 0.8365 (tmm) cc_final: 0.8023 (ppp) REVERT: A 966 MET cc_start: 0.7291 (ppp) cc_final: 0.7077 (ppp) REVERT: A 1066 MET cc_start: 0.6256 (pmm) cc_final: 0.5622 (mpp) REVERT: A 1108 MET cc_start: 0.5513 (mpp) cc_final: 0.5264 (mpp) outliers start: 34 outliers final: 19 residues processed: 133 average time/residue: 0.1848 time to fit residues: 36.6122 Evaluate side-chains 117 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.992 ------------------------------------------------------------------------------- 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 731 GLN 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 119 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 22 optimal weight: 0.0970 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 166 ASN A 854 HIS A 986 GLN ** A1137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1159 GLN ** A1204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1277 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.143563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.107075 restraints weight = 22038.566| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 4.16 r_work: 0.3612 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 9673 Z= 0.247 Angle : 0.698 9.965 13150 Z= 0.354 Chirality : 0.045 0.179 1488 Planarity : 0.005 0.056 1690 Dihedral : 5.390 32.881 1294 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.24 % Favored : 94.68 % Rotamer: Outliers : 4.38 % Allowed : 17.60 % Favored : 78.02 % 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: -1.78 (0.24), residues: 1202 helix: -0.97 (0.35), residues: 198 sheet: -0.35 (0.23), residues: 497 loop : -2.07 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1173 HIS 0.004 0.001 HIS A 914 PHE 0.028 0.002 PHE A1286 TYR 0.022 0.002 TYR A1135 ARG 0.005 0.000 ARG A1274 Details of bonding type rmsd hydrogen bonds : bond 0.03557 ( 383) hydrogen bonds : angle 5.74869 ( 1089) SS BOND : bond 0.00286 ( 10) SS BOND : angle 1.08311 ( 20) covalent geometry : bond 0.00560 ( 9663) covalent geometry : angle 0.69706 (13130) *********************** 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 144 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 98 time to evaluate : 1.021 Fit side-chains REVERT: A 144 MET cc_start: 0.8592 (mmt) cc_final: 0.8330 (mmt) REVERT: A 502 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7391 (mm-30) REVERT: A 522 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6753 (mm) REVERT: A 536 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8683 (mt) REVERT: A 555 GLU cc_start: 0.7959 (pp20) cc_final: 0.7463 (pp20) REVERT: A 601 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8788 (mm) REVERT: A 610 ARG cc_start: 0.8011 (tpm170) cc_final: 0.7749 (tpm170) REVERT: A 733 PHE cc_start: 0.7002 (OUTLIER) cc_final: 0.6331 (p90) REVERT: A 977 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7153 (pp) REVERT: A 1066 MET cc_start: 0.5953 (OUTLIER) cc_final: 0.5556 (mpp) REVERT: A 1108 MET cc_start: 0.5882 (mpp) cc_final: 0.5661 (mpp) outliers start: 46 outliers final: 30 residues processed: 130 average time/residue: 0.1844 time to fit residues: 35.7390 Evaluate side-chains 127 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 91 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN 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 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 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 615 MET Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 731 GLN 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 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 1232 TYR Chi-restraints excluded: chain A residue 1235 PHE 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 40 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 120 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 ASN A 986 GLN ** A1137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1204 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.144238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.108088 restraints weight = 21978.686| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 4.13 r_work: 0.3615 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9673 Z= 0.191 Angle : 0.638 13.497 13150 Z= 0.322 Chirality : 0.044 0.201 1488 Planarity : 0.004 0.042 1690 Dihedral : 5.171 31.018 1294 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.41 % Favored : 94.51 % Rotamer: Outliers : 4.95 % Allowed : 17.03 % Favored : 78.02 % 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: -1.62 (0.24), residues: 1202 helix: -0.65 (0.36), residues: 197 sheet: -0.33 (0.23), residues: 497 loop : -1.97 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1173 HIS 0.003 0.001 HIS A 914 PHE 0.035 0.002 PHE A 978 TYR 0.018 0.001 TYR A1135 ARG 0.003 0.000 ARG A1274 Details of bonding type rmsd hydrogen bonds : bond 0.03224 ( 383) hydrogen bonds : angle 5.54868 ( 1089) SS BOND : bond 0.00215 ( 10) SS BOND : angle 0.93286 ( 20) covalent geometry : bond 0.00434 ( 9663) covalent geometry : angle 0.63698 (13130) *********************** 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 155 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 103 time to evaluate : 0.966 Fit side-chains REVERT: A 464 CYS cc_start: 0.5031 (OUTLIER) cc_final: 0.4754 (p) REVERT: A 501 MET cc_start: 0.8229 (ttt) cc_final: 0.7882 (ttt) REVERT: A 522 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6731 (mm) REVERT: A 536 ILE cc_start: 0.8996 (OUTLIER) cc_final: 0.8623 (mp) REVERT: A 601 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8780 (mm) REVERT: A 610 ARG cc_start: 0.7917 (tpm170) cc_final: 0.7633 (tpm170) REVERT: A 733 PHE cc_start: 0.7172 (OUTLIER) cc_final: 0.6903 (p90) REVERT: A 977 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7188 (pp) REVERT: A 1066 MET cc_start: 0.6093 (OUTLIER) cc_final: 0.5572 (mpp) REVERT: A 1272 PHE cc_start: 0.7950 (t80) cc_final: 0.7649 (t80) outliers start: 52 outliers final: 30 residues processed: 139 average time/residue: 0.1778 time to fit residues: 36.9238 Evaluate side-chains 133 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 96 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 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 181 VAL Chi-restraints excluded: chain A residue 325 VAL 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 464 CYS 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 731 GLN 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 1066 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 41 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 87 optimal weight: 0.0870 chunk 55 optimal weight: 0.8980 chunk 95 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 90 optimal weight: 6.9990 chunk 51 optimal weight: 0.3980 chunk 56 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 986 GLN A1159 GLN A1277 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.145662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.112624 restraints weight = 21792.670| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 4.60 r_work: 0.3638 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9673 Z= 0.124 Angle : 0.609 14.347 13150 Z= 0.304 Chirality : 0.044 0.194 1488 Planarity : 0.004 0.044 1690 Dihedral : 4.892 29.756 1294 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.74 % Favored : 95.17 % Rotamer: Outliers : 4.38 % Allowed : 17.70 % 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: -1.38 (0.24), residues: 1202 helix: -0.33 (0.37), residues: 201 sheet: -0.21 (0.23), residues: 497 loop : -1.84 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1173 HIS 0.002 0.000 HIS A 914 PHE 0.023 0.001 PHE A1286 TYR 0.013 0.001 TYR A1135 ARG 0.003 0.000 ARG A1274 Details of bonding type rmsd hydrogen bonds : bond 0.02921 ( 383) hydrogen bonds : angle 5.31633 ( 1089) SS BOND : bond 0.00157 ( 10) SS BOND : angle 0.81796 ( 20) covalent geometry : bond 0.00284 ( 9663) covalent geometry : angle 0.60850 (13130) *********************** 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 150 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 104 time to evaluate : 0.979 Fit side-chains REVERT: A 162 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7344 (m-30) REVERT: A 464 CYS cc_start: 0.4817 (OUTLIER) cc_final: 0.4457 (p) REVERT: A 501 MET cc_start: 0.8170 (ttt) cc_final: 0.7936 (ttt) REVERT: A 522 LEU cc_start: 0.7200 (OUTLIER) cc_final: 0.6773 (mm) REVERT: A 536 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8559 (mp) REVERT: A 537 TYR cc_start: 0.8617 (p90) cc_final: 0.8344 (p90) REVERT: A 601 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8728 (mm) REVERT: A 733 PHE cc_start: 0.7254 (OUTLIER) cc_final: 0.7053 (p90) REVERT: A 977 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7164 (pp) REVERT: A 1066 MET cc_start: 0.6103 (OUTLIER) cc_final: 0.5484 (mpp) REVERT: A 1069 ASN cc_start: 0.6950 (m-40) cc_final: 0.6487 (m110) REVERT: A 1108 MET cc_start: 0.5733 (mpp) cc_final: 0.5427 (mpp) REVERT: A 1215 ILE cc_start: 0.5417 (OUTLIER) cc_final: 0.4672 (mt) REVERT: A 1272 PHE cc_start: 0.7935 (t80) cc_final: 0.7575 (t80) outliers start: 46 outliers final: 27 residues processed: 139 average time/residue: 0.1700 time to fit residues: 35.5697 Evaluate side-chains 131 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 95 time to evaluate : 1.479 ------------------------------------------------------------------------------- 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 380 ILE Chi-restraints excluded: chain A residue 464 CYS Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 522 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 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 1066 MET 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 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 99 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 105 optimal weight: 9.9990 chunk 70 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 986 GLN ** A1137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.143393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.107587 restraints weight = 21991.375| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 4.02 r_work: 0.3606 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 9673 Z= 0.198 Angle : 0.652 14.309 13150 Z= 0.326 Chirality : 0.044 0.195 1488 Planarity : 0.004 0.046 1690 Dihedral : 5.044 30.493 1294 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.91 % Favored : 94.01 % Rotamer: Outliers : 4.66 % Allowed : 17.98 % Favored : 77.35 % 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: -1.39 (0.24), residues: 1202 helix: -0.33 (0.37), residues: 201 sheet: -0.25 (0.23), residues: 497 loop : -1.81 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1173 HIS 0.003 0.001 HIS A 914 PHE 0.034 0.002 PHE A1286 TYR 0.014 0.001 TYR A1135 ARG 0.003 0.000 ARG A1274 Details of bonding type rmsd hydrogen bonds : bond 0.03177 ( 383) hydrogen bonds : angle 5.42723 ( 1089) SS BOND : bond 0.00239 ( 10) SS BOND : angle 0.89648 ( 20) covalent geometry : bond 0.00453 ( 9663) covalent geometry : angle 0.65114 (13130) *********************** 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 150 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 101 time to evaluate : 0.993 Fit side-chains REVERT: A 342 MET cc_start: 0.6355 (OUTLIER) cc_final: 0.6117 (ppp) REVERT: A 464 CYS cc_start: 0.4853 (OUTLIER) cc_final: 0.4623 (p) REVERT: A 501 MET cc_start: 0.8244 (ttt) cc_final: 0.7997 (ttt) REVERT: A 522 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.6806 (mm) REVERT: A 536 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8626 (mt) REVERT: A 537 TYR cc_start: 0.8596 (p90) cc_final: 0.8284 (p90) REVERT: A 601 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8792 (mm) REVERT: A 610 ARG cc_start: 0.7983 (tpm170) cc_final: 0.7618 (tpm170) REVERT: A 733 PHE cc_start: 0.7520 (OUTLIER) cc_final: 0.7061 (p90) REVERT: A 1066 MET cc_start: 0.6016 (OUTLIER) cc_final: 0.5312 (mpp) REVERT: A 1069 ASN cc_start: 0.6978 (m-40) cc_final: 0.6524 (m110) outliers start: 49 outliers final: 32 residues processed: 137 average time/residue: 0.1697 time to fit residues: 34.9750 Evaluate side-chains 135 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 96 time to evaluate : 0.990 ------------------------------------------------------------------------------- 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 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 464 CYS Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 522 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 731 GLN 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 1066 MET Chi-restraints excluded: chain A residue 1113 ASP Chi-restraints excluded: chain A residue 1199 TYR Chi-restraints excluded: chain A residue 1235 PHE Chi-restraints excluded: chain A residue 1287 GLN Chi-restraints excluded: chain A residue 1290 THR 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 81 optimal weight: 5.9990 chunk 107 optimal weight: 0.0980 chunk 40 optimal weight: 0.4980 chunk 78 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 18 optimal weight: 0.0970 chunk 90 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.144432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.108556 restraints weight = 22047.553| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 4.09 r_work: 0.3619 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9673 Z= 0.152 Angle : 0.634 17.248 13150 Z= 0.314 Chirality : 0.044 0.195 1488 Planarity : 0.004 0.047 1690 Dihedral : 4.918 30.143 1294 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.07 % Favored : 94.84 % Rotamer: Outliers : 4.19 % Allowed : 18.55 % Favored : 77.26 % 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: -1.31 (0.24), residues: 1202 helix: -0.19 (0.37), residues: 198 sheet: -0.20 (0.23), residues: 495 loop : -1.78 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1173 HIS 0.002 0.000 HIS A 914 PHE 0.021 0.001 PHE A1272 TYR 0.014 0.001 TYR A1142 ARG 0.002 0.000 ARG A1274 Details of bonding type rmsd hydrogen bonds : bond 0.02954 ( 383) hydrogen bonds : angle 5.30099 ( 1089) SS BOND : bond 0.00189 ( 10) SS BOND : angle 0.83150 ( 20) covalent geometry : bond 0.00350 ( 9663) covalent geometry : angle 0.63399 (13130) *********************** 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 147 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 103 time to evaluate : 1.077 Fit side-chains REVERT: A 114 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8278 (tp) REVERT: A 162 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7418 (m-30) REVERT: A 342 MET cc_start: 0.6619 (OUTLIER) cc_final: 0.6364 (ppp) REVERT: A 464 CYS cc_start: 0.4802 (OUTLIER) cc_final: 0.4540 (p) REVERT: A 501 MET cc_start: 0.8295 (ttt) cc_final: 0.8037 (ttt) REVERT: A 522 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.6921 (mm) REVERT: A 536 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8556 (mt) REVERT: A 537 TYR cc_start: 0.8568 (p90) cc_final: 0.8346 (p90) REVERT: A 601 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8718 (mm) REVERT: A 610 ARG cc_start: 0.7938 (tpm170) cc_final: 0.7713 (tpm170) REVERT: A 733 PHE cc_start: 0.7542 (OUTLIER) cc_final: 0.7087 (p90) REVERT: A 1066 MET cc_start: 0.6067 (OUTLIER) cc_final: 0.5350 (mpp) REVERT: A 1069 ASN cc_start: 0.6944 (m-40) cc_final: 0.6527 (m110) REVERT: A 1215 ILE cc_start: 0.5578 (OUTLIER) cc_final: 0.4799 (mt) REVERT: A 1288 GLN cc_start: 0.8582 (pp30) cc_final: 0.8028 (pp30) outliers start: 44 outliers final: 28 residues processed: 135 average time/residue: 0.1773 time to fit residues: 36.2201 Evaluate side-chains 138 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 100 time to evaluate : 1.146 ------------------------------------------------------------------------------- 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 114 LEU 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 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 464 CYS Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 522 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 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 1066 MET 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 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 30 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 103 optimal weight: 0.0570 chunk 52 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 61 optimal weight: 0.6980 overall best weight: 1.3300 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.143087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.109709 restraints weight = 22100.729| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 4.86 r_work: 0.3593 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9673 Z= 0.191 Angle : 0.668 15.075 13150 Z= 0.330 Chirality : 0.045 0.271 1488 Planarity : 0.004 0.046 1690 Dihedral : 5.014 30.655 1294 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.99 % Favored : 93.93 % Rotamer: Outliers : 4.85 % Allowed : 18.46 % Favored : 76.69 % 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: -1.30 (0.24), residues: 1202 helix: -0.06 (0.37), residues: 193 sheet: -0.25 (0.23), residues: 495 loop : -1.76 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1173 HIS 0.002 0.001 HIS A 914 PHE 0.037 0.002 PHE A1286 TYR 0.016 0.001 TYR A1142 ARG 0.002 0.000 ARG A1274 Details of bonding type rmsd hydrogen bonds : bond 0.03089 ( 383) hydrogen bonds : angle 5.38634 ( 1089) SS BOND : bond 0.00233 ( 10) SS BOND : angle 0.87817 ( 20) covalent geometry : bond 0.00441 ( 9663) covalent geometry : angle 0.66790 (13130) *********************** 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 150 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 99 time to evaluate : 1.308 Fit side-chains REVERT: A 66 LEU cc_start: 0.8457 (tp) cc_final: 0.8146 (mp) REVERT: A 114 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8264 (tp) REVERT: A 144 MET cc_start: 0.8172 (mmt) cc_final: 0.7284 (mmt) REVERT: A 177 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7784 (pm20) REVERT: A 342 MET cc_start: 0.6361 (OUTLIER) cc_final: 0.6107 (ppp) REVERT: A 464 CYS cc_start: 0.4868 (OUTLIER) cc_final: 0.4569 (p) REVERT: A 501 MET cc_start: 0.8237 (ttt) cc_final: 0.7987 (ttt) REVERT: A 536 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8594 (mt) REVERT: A 537 TYR cc_start: 0.8578 (p90) cc_final: 0.8354 (p90) REVERT: A 601 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8619 (mm) REVERT: A 610 ARG cc_start: 0.7973 (tpm170) cc_final: 0.7713 (tpm170) REVERT: A 733 PHE cc_start: 0.7782 (OUTLIER) cc_final: 0.7194 (p90) REVERT: A 1066 MET cc_start: 0.6066 (OUTLIER) cc_final: 0.5362 (mpp) REVERT: A 1069 ASN cc_start: 0.6997 (m-40) cc_final: 0.6527 (m110) REVERT: A 1288 GLN cc_start: 0.8635 (pp30) cc_final: 0.8086 (pp30) outliers start: 51 outliers final: 34 residues processed: 139 average time/residue: 0.1929 time to fit residues: 40.5295 Evaluate side-chains 140 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 98 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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 114 LEU 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 464 CYS Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 502 GLU 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 731 GLN Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 793 ASP 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 1066 MET 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 1235 PHE Chi-restraints excluded: chain A residue 1287 GLN Chi-restraints excluded: chain A residue 1290 THR 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 84 optimal weight: 6.9990 chunk 98 optimal weight: 0.0670 chunk 115 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 119 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 90 optimal weight: 8.9990 chunk 120 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 overall best weight: 1.1322 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.143909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.108212 restraints weight = 21891.993| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 4.02 r_work: 0.3613 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9673 Z= 0.170 Angle : 0.653 13.987 13150 Z= 0.323 Chirality : 0.044 0.209 1488 Planarity : 0.004 0.047 1690 Dihedral : 4.951 30.304 1294 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.66 % Favored : 94.26 % Rotamer: Outliers : 4.28 % Allowed : 19.31 % Favored : 76.40 % 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: -1.25 (0.24), residues: 1202 helix: 0.04 (0.38), residues: 192 sheet: -0.24 (0.23), residues: 494 loop : -1.72 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A1173 HIS 0.002 0.001 HIS A 914 PHE 0.021 0.002 PHE A1286 TYR 0.016 0.001 TYR A1142 ARG 0.004 0.000 ARG A 602 Details of bonding type rmsd hydrogen bonds : bond 0.03010 ( 383) hydrogen bonds : angle 5.34105 ( 1089) SS BOND : bond 0.00215 ( 10) SS BOND : angle 0.86775 ( 20) covalent geometry : bond 0.00392 ( 9663) covalent geometry : angle 0.65264 (13130) *********************** 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 145 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 100 time to evaluate : 1.147 Fit side-chains REVERT: A 114 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8237 (tp) REVERT: A 177 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7822 (pm20) REVERT: A 342 MET cc_start: 0.6638 (OUTLIER) cc_final: 0.6389 (ppp) REVERT: A 464 CYS cc_start: 0.4758 (OUTLIER) cc_final: 0.4506 (p) REVERT: A 536 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8674 (mp) REVERT: A 601 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8630 (mm) REVERT: A 610 ARG cc_start: 0.7956 (tpm170) cc_final: 0.7682 (tpm170) REVERT: A 1066 MET cc_start: 0.6067 (OUTLIER) cc_final: 0.5360 (mpp) REVERT: A 1069 ASN cc_start: 0.7144 (m-40) cc_final: 0.6713 (m110) REVERT: A 1288 GLN cc_start: 0.8623 (pp30) cc_final: 0.8044 (pp30) outliers start: 45 outliers final: 34 residues processed: 135 average time/residue: 0.1755 time to fit residues: 35.9404 Evaluate side-chains 135 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 94 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 114 LEU 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 464 CYS Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 598 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 733 PHE Chi-restraints excluded: chain A residue 793 ASP 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 1066 MET 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 1235 PHE Chi-restraints excluded: chain A residue 1287 GLN Chi-restraints excluded: chain A residue 1290 THR 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 104 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 0.0570 chunk 68 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 20 optimal weight: 0.1980 chunk 89 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 34 optimal weight: 8.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.145268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.109920 restraints weight = 22028.330| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 4.06 r_work: 0.3641 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9673 Z= 0.127 Angle : 0.632 13.338 13150 Z= 0.311 Chirality : 0.044 0.210 1488 Planarity : 0.004 0.047 1690 Dihedral : 4.783 28.652 1294 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.57 % Favored : 94.34 % Rotamer: Outliers : 3.33 % Allowed : 20.27 % Favored : 76.40 % 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: -1.11 (0.24), residues: 1202 helix: 0.26 (0.39), residues: 190 sheet: -0.15 (0.23), residues: 494 loop : -1.67 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A1173 HIS 0.002 0.000 HIS A 914 PHE 0.034 0.001 PHE A1286 TYR 0.015 0.001 TYR A1142 ARG 0.003 0.000 ARG A 602 Details of bonding type rmsd hydrogen bonds : bond 0.02788 ( 383) hydrogen bonds : angle 5.18355 ( 1089) SS BOND : bond 0.00164 ( 10) SS BOND : angle 0.75080 ( 20) covalent geometry : bond 0.00297 ( 9663) covalent geometry : angle 0.63198 (13130) ********************** 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 135 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 100 time to evaluate : 0.993 Fit side-chains REVERT: A 66 LEU cc_start: 0.8365 (tp) cc_final: 0.8146 (mp) REVERT: A 144 MET cc_start: 0.7907 (mmt) cc_final: 0.7472 (mmt) REVERT: A 177 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7811 (pm20) REVERT: A 339 MET cc_start: 0.6777 (tmm) cc_final: 0.6383 (tmm) REVERT: A 342 MET cc_start: 0.6745 (OUTLIER) cc_final: 0.6494 (ppp) REVERT: A 377 PHE cc_start: 0.6914 (t80) cc_final: 0.6706 (t80) REVERT: A 536 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8582 (mp) REVERT: A 601 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8485 (mm) REVERT: A 610 ARG cc_start: 0.7951 (tpm170) cc_final: 0.7674 (tpm170) REVERT: A 975 MET cc_start: 0.0159 (tmm) cc_final: -0.0526 (tpt) REVERT: A 1215 ILE cc_start: 0.5443 (OUTLIER) cc_final: 0.4668 (mt) outliers start: 35 outliers final: 27 residues processed: 126 average time/residue: 0.1694 time to fit residues: 32.2048 Evaluate side-chains 126 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 94 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 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 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 502 GLU Chi-restraints excluded: chain A residue 536 ILE 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 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 1113 ASP Chi-restraints excluded: chain A residue 1171 ILE 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 1290 THR 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 30 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 40 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.144636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.112576 restraints weight = 21820.849| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 4.47 r_work: 0.3620 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9673 Z= 0.146 Angle : 0.649 14.873 13150 Z= 0.318 Chirality : 0.044 0.203 1488 Planarity : 0.004 0.048 1690 Dihedral : 4.779 29.207 1294 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.49 % Favored : 94.43 % Rotamer: Outliers : 3.62 % Allowed : 20.27 % Favored : 76.12 % 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: -1.10 (0.24), residues: 1202 helix: 0.23 (0.39), residues: 191 sheet: -0.15 (0.24), residues: 494 loop : -1.65 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1173 HIS 0.002 0.000 HIS A 77 PHE 0.020 0.001 PHE A1286 TYR 0.016 0.001 TYR A 537 ARG 0.004 0.000 ARG A 602 Details of bonding type rmsd hydrogen bonds : bond 0.02838 ( 383) hydrogen bonds : angle 5.19550 ( 1089) SS BOND : bond 0.00225 ( 10) SS BOND : angle 0.74169 ( 20) covalent geometry : bond 0.00341 ( 9663) covalent geometry : angle 0.64923 (13130) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5901.09 seconds wall clock time: 101 minutes 40.82 seconds (6100.82 seconds total)