Starting phenix.real_space_refine on Tue Apr 29 18:31:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9juo_61832/04_2025/9juo_61832.cif Found real_map, /net/cci-nas-00/data/ceres_data/9juo_61832/04_2025/9juo_61832.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9juo_61832/04_2025/9juo_61832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9juo_61832/04_2025/9juo_61832.map" model { file = "/net/cci-nas-00/data/ceres_data/9juo_61832/04_2025/9juo_61832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9juo_61832/04_2025/9juo_61832.cif" } resolution = 3.1 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= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 40 5.16 5 C 5645 2.51 5 N 1518 2.21 5 O 1647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8858 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1144, 8794 Classifications: {'peptide': 1144} Link IDs: {'PTRANS': 29, 'TRANS': 1114} Chain breaks: 1 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ANP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 5.68, per 1000 atoms: 0.64 Number of scatterers: 8858 At special positions: 0 Unit cell: (106.02, 102.3, 126.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 40 16.00 P 6 15.00 Mg 2 11.99 O 1647 8.00 N 1518 7.00 C 5645 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 1.1 seconds 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 5 sheets defined 67.6% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 28 through 34 Processing helix chain 'A' and resid 37 through 74 removed outlier: 4.268A pdb=" N LEU A 58 " --> pdb=" O HIS A 54 " (cutoff:3.500A) Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 78 through 132 Processing helix chain 'A' and resid 135 through 139 Processing helix chain 'A' and resid 143 through 162 removed outlier: 4.397A pdb=" N ALA A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N VAL A 156 " --> pdb=" O ASN A 152 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASP A 160 " --> pdb=" O VAL A 156 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE A 162 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 187 Processing helix chain 'A' and resid 187 through 236 Proline residue: A 199 - end of helix Processing helix chain 'A' and resid 236 through 243 removed outlier: 3.746A pdb=" N ALA A 242 " --> pdb=" O ARG A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 299 Processing helix chain 'A' and resid 303 through 324 Processing helix chain 'A' and resid 324 through 347 removed outlier: 3.587A pdb=" N HIS A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 355 Processing helix chain 'A' and resid 408 through 417 Processing helix chain 'A' and resid 435 through 437 No H-bonds generated for 'chain 'A' and resid 435 through 437' Processing helix chain 'A' and resid 440 through 446 Processing helix chain 'A' and resid 459 through 466 Processing helix chain 'A' and resid 472 through 483 removed outlier: 3.539A pdb=" N ALA A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 491 removed outlier: 3.776A pdb=" N ILE A 490 " --> pdb=" O HIS A 486 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS A 491 " --> pdb=" O SER A 487 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 486 through 491' Processing helix chain 'A' and resid 509 through 523 removed outlier: 3.662A pdb=" N GLN A 513 " --> pdb=" O GLY A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 547 Processing helix chain 'A' and resid 577 through 581 Processing helix chain 'A' and resid 678 through 693 Processing helix chain 'A' and resid 696 through 729 removed outlier: 3.639A pdb=" N ALA A 700 " --> pdb=" O GLU A 696 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR A 729 " --> pdb=" O LEU A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 785 Processing helix chain 'A' and resid 788 through 794 Processing helix chain 'A' and resid 798 through 842 removed outlier: 4.313A pdb=" N ARG A 820 " --> pdb=" O ALA A 816 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ILE A 821 " --> pdb=" O ILE A 817 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER A 822 " --> pdb=" O GLY A 818 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL A 823 " --> pdb=" O ASP A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 852 Processing helix chain 'A' and resid 852 through 869 Processing helix chain 'A' and resid 873 through 878 Processing helix chain 'A' and resid 878 through 891 Processing helix chain 'A' and resid 891 through 898 Processing helix chain 'A' and resid 900 through 954 Proline residue: A 914 - end of helix Processing helix chain 'A' and resid 958 through 1001 Proline residue: A 984 - end of helix Processing helix chain 'A' and resid 1065 through 1070 removed outlier: 3.659A pdb=" N ILE A1069 " --> pdb=" O LYS A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1095 through 1100 Processing helix chain 'A' and resid 1115 through 1122 Processing helix chain 'A' and resid 1129 through 1134 Processing helix chain 'A' and resid 1135 through 1139 Processing helix chain 'A' and resid 1142 through 1148 Processing helix chain 'A' and resid 1150 through 1154 removed outlier: 3.529A pdb=" N THR A1154 " --> pdb=" O GLY A1151 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1180 Processing helix chain 'A' and resid 1194 through 1209 Processing sheet with id=AA1, first strand: chain 'A' and resid 368 through 369 Processing sheet with id=AA2, first strand: chain 'A' and resid 398 through 399 removed outlier: 7.279A pdb=" N LEU A 528 " --> pdb=" O THR A 557 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1040 through 1049 removed outlier: 4.123A pdb=" N ARG A1043 " --> pdb=" O ILE A1029 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE A1029 " --> pdb=" O ARG A1043 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU A1045 " --> pdb=" O LYS A1027 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS A1027 " --> pdb=" O LEU A1045 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU A1047 " --> pdb=" O GLU A1025 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLU A1025 " --> pdb=" O LEU A1047 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1054 through 1055 removed outlier: 6.146A pdb=" N ALA A1103 " --> pdb=" O LEU A1185 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1233 through 1234 600 hydrogen bonds defined for protein. 1755 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: 3.19 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2301 1.33 - 1.45: 1596 1.45 - 1.57: 5048 1.57 - 1.69: 10 1.69 - 1.81: 66 Bond restraints: 9021 Sorted by residual: bond pdb=" N3B ANP A1303 " pdb=" PG ANP A1303 " ideal model delta sigma weight residual 1.795 1.634 0.161 2.00e-02 2.50e+03 6.50e+01 bond pdb=" N3B ANP A1304 " pdb=" PG ANP A1304 " ideal model delta sigma weight residual 1.795 1.634 0.161 2.00e-02 2.50e+03 6.50e+01 bond pdb=" O3A ANP A1303 " pdb=" PB ANP A1303 " ideal model delta sigma weight residual 1.700 1.601 0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" O3A ANP A1304 " pdb=" PB ANP A1304 " ideal model delta sigma weight residual 1.700 1.603 0.097 2.00e-02 2.50e+03 2.35e+01 bond pdb=" N ILE A 821 " pdb=" CA ILE A 821 " ideal model delta sigma weight residual 1.461 1.497 -0.035 1.17e-02 7.31e+03 9.12e+00 ... (remaining 9016 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 11838 1.95 - 3.90: 342 3.90 - 5.85: 35 5.85 - 7.80: 7 7.80 - 9.75: 3 Bond angle restraints: 12225 Sorted by residual: angle pdb=" CA TRP A 843 " pdb=" C TRP A 843 " pdb=" O TRP A 843 " ideal model delta sigma weight residual 121.99 117.68 4.31 1.14e+00 7.69e-01 1.43e+01 angle pdb=" N VAL A 813 " pdb=" CA VAL A 813 " pdb=" C VAL A 813 " ideal model delta sigma weight residual 110.62 106.81 3.81 1.02e+00 9.61e-01 1.40e+01 angle pdb=" N GLU A1203 " pdb=" CA GLU A1203 " pdb=" CB GLU A1203 " ideal model delta sigma weight residual 110.16 115.30 -5.14 1.48e+00 4.57e-01 1.20e+01 angle pdb=" C VAL A 198 " pdb=" CA VAL A 198 " pdb=" CB VAL A 198 " ideal model delta sigma weight residual 113.70 110.41 3.29 9.50e-01 1.11e+00 1.20e+01 angle pdb=" CA VAL A 823 " pdb=" C VAL A 823 " pdb=" O VAL A 823 " ideal model delta sigma weight residual 121.17 117.64 3.53 1.06e+00 8.90e-01 1.11e+01 ... (remaining 12220 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.85: 5182 28.85 - 57.70: 181 57.70 - 86.56: 49 86.56 - 115.41: 3 115.41 - 144.26: 1 Dihedral angle restraints: 5416 sinusoidal: 2124 harmonic: 3292 Sorted by residual: dihedral pdb=" O1A ANP A1303 " pdb=" O3A ANP A1303 " pdb=" PA ANP A1303 " pdb=" PB ANP A1303 " ideal model delta sinusoidal sigma weight residual 83.11 -61.15 144.26 1 3.00e+01 1.11e-03 1.93e+01 dihedral pdb=" O1B ANP A1304 " pdb=" N3B ANP A1304 " pdb=" PB ANP A1304 " pdb=" PG ANP A1304 " ideal model delta sinusoidal sigma weight residual 35.15 -62.81 97.96 1 3.00e+01 1.11e-03 1.21e+01 dihedral pdb=" CA ARG A1099 " pdb=" C ARG A1099 " pdb=" N LYS A1100 " pdb=" CA LYS A1100 " ideal model delta harmonic sigma weight residual 180.00 162.82 17.18 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 5413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1230 0.067 - 0.135: 155 0.135 - 0.202: 23 0.202 - 0.270: 1 0.270 - 0.337: 2 Chirality restraints: 1411 Sorted by residual: chirality pdb=" C3' ANP A1304 " pdb=" C2' ANP A1304 " pdb=" C4' ANP A1304 " pdb=" O3' ANP A1304 " both_signs ideal model delta sigma weight residual False -2.36 -2.69 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" C3' ANP A1303 " pdb=" C2' ANP A1303 " pdb=" C4' ANP A1303 " pdb=" O3' ANP A1303 " both_signs ideal model delta sigma weight residual False -2.36 -2.69 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CA LEU A 806 " pdb=" N LEU A 806 " pdb=" C LEU A 806 " pdb=" CB LEU A 806 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 1408 not shown) Planarity restraints: 1542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A1036 " 0.215 9.50e-02 1.11e+02 9.65e-02 5.72e+00 pdb=" NE ARG A1036 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A1036 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A1036 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A1036 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 708 " -0.010 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" C VAL A 708 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL A 708 " -0.012 2.00e-02 2.50e+03 pdb=" N ILE A 709 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 711 " -0.009 2.00e-02 2.50e+03 1.72e-02 2.96e+00 pdb=" C GLY A 711 " 0.030 2.00e-02 2.50e+03 pdb=" O GLY A 711 " -0.011 2.00e-02 2.50e+03 pdb=" N SER A 712 " -0.010 2.00e-02 2.50e+03 ... (remaining 1539 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 95 2.62 - 3.19: 8589 3.19 - 3.76: 14593 3.76 - 4.33: 19174 4.33 - 4.90: 31410 Nonbonded interactions: 73861 Sorted by model distance: nonbonded pdb=" OG SER A 410 " pdb="MG MG A1301 " model vdw 2.047 2.170 nonbonded pdb=" OG1 THR A 140 " pdb=" OE1 GLU A 141 " model vdw 2.160 3.040 nonbonded pdb=" OD2 ASP A 531 " pdb="MG MG A1301 " model vdw 2.168 2.170 nonbonded pdb=" OD1 ASP A 531 " pdb="MG MG A1301 " model vdw 2.190 2.170 nonbonded pdb=" NE2 GLN A1107 " pdb="MG MG A1302 " model vdw 2.191 2.250 ... (remaining 73856 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: 0.010 Normalize map: mean=0, sd=1: 1.310 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: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 24.800 Find NCS groups from input model: 0.110 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: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.161 9021 Z= 0.336 Angle : 0.699 9.751 12225 Z= 0.444 Chirality : 0.049 0.337 1411 Planarity : 0.005 0.096 1542 Dihedral : 16.179 144.260 3298 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.43 % Allowed : 0.86 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.26), residues: 1140 helix: 1.73 (0.20), residues: 718 sheet: -1.98 (0.79), residues: 43 loop : -1.65 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 188 HIS 0.003 0.001 HIS A 171 PHE 0.024 0.001 PHE A 686 TYR 0.015 0.001 TYR A1093 ARG 0.004 0.000 ARG A1099 Details of bonding type rmsd hydrogen bonds : bond 0.12698 ( 600) hydrogen bonds : angle 5.37283 ( 1755) covalent geometry : bond 0.00532 ( 9021) covalent geometry : angle 0.69881 (12225) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 144 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 SER cc_start: 0.8755 (t) cc_final: 0.8515 (p) REVERT: A 461 LYS cc_start: 0.6358 (mmtt) cc_final: 0.6125 (mmtt) outliers start: 4 outliers final: 0 residues processed: 146 average time/residue: 0.2154 time to fit residues: 44.3345 Evaluate side-chains 96 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.4980 chunk 86 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 34 optimal weight: 8.9990 chunk 54 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 GLN A 323 GLN A 445 GLN A 451 GLN A 826 GLN A 827 ASN A1142 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.166500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.114104 restraints weight = 12001.736| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.48 r_work: 0.3211 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9021 Z= 0.135 Angle : 0.550 8.633 12225 Z= 0.287 Chirality : 0.040 0.141 1411 Planarity : 0.004 0.066 1542 Dihedral : 10.476 139.012 1294 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.86 % Allowed : 9.25 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.26), residues: 1140 helix: 2.24 (0.19), residues: 722 sheet: -2.14 (0.71), residues: 49 loop : -1.56 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 441 HIS 0.006 0.001 HIS A1228 PHE 0.011 0.001 PHE A 792 TYR 0.014 0.001 TYR A1117 ARG 0.004 0.000 ARG A1099 Details of bonding type rmsd hydrogen bonds : bond 0.05476 ( 600) hydrogen bonds : angle 4.29959 ( 1755) covalent geometry : bond 0.00270 ( 9021) covalent geometry : angle 0.55036 (12225) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.9357 (ttm) cc_final: 0.9096 (ttm) REVERT: A 780 MET cc_start: 0.9038 (mtp) cc_final: 0.8742 (mtm) REVERT: A 1001 ASP cc_start: 0.7652 (m-30) cc_final: 0.7447 (m-30) REVERT: A 1084 MET cc_start: 0.7328 (tpp) cc_final: 0.6975 (tpt) outliers start: 8 outliers final: 2 residues processed: 113 average time/residue: 0.2185 time to fit residues: 35.0124 Evaluate side-chains 98 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 96 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 528 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 25 optimal weight: 5.9990 chunk 74 optimal weight: 0.0470 chunk 107 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 103 optimal weight: 0.0670 chunk 15 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.1620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 GLN A 323 GLN A 445 GLN A 451 GLN A 842 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.164641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.111501 restraints weight = 12186.385| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.28 r_work: 0.3189 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9021 Z= 0.142 Angle : 0.534 8.435 12225 Z= 0.283 Chirality : 0.040 0.143 1411 Planarity : 0.004 0.048 1542 Dihedral : 8.711 142.120 1294 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.26 % Allowed : 12.04 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.26), residues: 1140 helix: 2.20 (0.19), residues: 722 sheet: -2.12 (0.72), residues: 49 loop : -1.51 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 441 HIS 0.008 0.002 HIS A1228 PHE 0.010 0.001 PHE A 72 TYR 0.010 0.001 TYR A1117 ARG 0.007 0.000 ARG A1212 Details of bonding type rmsd hydrogen bonds : bond 0.05372 ( 600) hydrogen bonds : angle 4.19710 ( 1755) covalent geometry : bond 0.00304 ( 9021) covalent geometry : angle 0.53393 (12225) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.967 Fit side-chains REVERT: A 801 ARG cc_start: 0.7476 (ttp-170) cc_final: 0.7169 (ttm110) REVERT: A 1001 ASP cc_start: 0.7652 (m-30) cc_final: 0.7449 (m-30) REVERT: A 1084 MET cc_start: 0.7174 (tpp) cc_final: 0.6935 (tpt) outliers start: 21 outliers final: 11 residues processed: 122 average time/residue: 0.1978 time to fit residues: 34.7927 Evaluate side-chains 114 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 686 PHE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 1058 VAL Chi-restraints excluded: chain A residue 1069 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 96 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 GLN A 451 GLN A 511 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.163085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.110215 restraints weight = 12064.549| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.53 r_work: 0.3156 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9021 Z= 0.160 Angle : 0.538 10.184 12225 Z= 0.288 Chirality : 0.040 0.134 1411 Planarity : 0.004 0.043 1542 Dihedral : 8.356 139.510 1294 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.26 % Allowed : 13.66 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.25), residues: 1140 helix: 2.14 (0.19), residues: 719 sheet: -1.96 (0.73), residues: 49 loop : -1.52 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 441 HIS 0.008 0.002 HIS A1228 PHE 0.009 0.001 PHE A 72 TYR 0.012 0.001 TYR A 89 ARG 0.005 0.000 ARG A1212 Details of bonding type rmsd hydrogen bonds : bond 0.05543 ( 600) hydrogen bonds : angle 4.23440 ( 1755) covalent geometry : bond 0.00357 ( 9021) covalent geometry : angle 0.53831 (12225) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.766 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.9413 (ttm) cc_final: 0.9119 (ttm) REVERT: A 141 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6838 (mp0) outliers start: 21 outliers final: 14 residues processed: 110 average time/residue: 0.2398 time to fit residues: 38.0862 Evaluate side-chains 112 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 686 PHE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 1058 VAL Chi-restraints excluded: chain A residue 1069 ILE Chi-restraints excluded: chain A residue 1071 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 35 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 GLN A 693 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.159939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.107010 restraints weight = 12205.846| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.57 r_work: 0.3120 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9021 Z= 0.197 Angle : 0.564 9.844 12225 Z= 0.303 Chirality : 0.041 0.131 1411 Planarity : 0.004 0.042 1542 Dihedral : 8.390 137.297 1294 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.58 % Allowed : 14.95 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.25), residues: 1140 helix: 1.94 (0.19), residues: 720 sheet: -1.85 (0.74), residues: 49 loop : -1.52 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 441 HIS 0.008 0.002 HIS A1228 PHE 0.013 0.002 PHE A1075 TYR 0.013 0.002 TYR A 89 ARG 0.003 0.000 ARG A1212 Details of bonding type rmsd hydrogen bonds : bond 0.05938 ( 600) hydrogen bonds : angle 4.33090 ( 1755) covalent geometry : bond 0.00452 ( 9021) covalent geometry : angle 0.56369 (12225) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 0.906 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.9405 (ttm) cc_final: 0.9049 (ttm) REVERT: A 141 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6888 (mp0) outliers start: 24 outliers final: 16 residues processed: 111 average time/residue: 0.2006 time to fit residues: 31.8361 Evaluate side-chains 114 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 686 PHE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 1058 VAL Chi-restraints excluded: chain A residue 1069 ILE Chi-restraints excluded: chain A residue 1071 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 65 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 108 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 chunk 21 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 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 251 GLN A 451 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.163396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.111120 restraints weight = 12189.978| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.43 r_work: 0.3175 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9021 Z= 0.132 Angle : 0.536 10.342 12225 Z= 0.285 Chirality : 0.039 0.158 1411 Planarity : 0.004 0.037 1542 Dihedral : 8.198 137.700 1294 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.47 % Allowed : 15.91 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.25), residues: 1140 helix: 2.15 (0.19), residues: 720 sheet: -1.78 (0.75), residues: 49 loop : -1.48 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 441 HIS 0.008 0.001 HIS A1228 PHE 0.012 0.001 PHE A 488 TYR 0.018 0.001 TYR A1093 ARG 0.003 0.000 ARG A1099 Details of bonding type rmsd hydrogen bonds : bond 0.05304 ( 600) hydrogen bonds : angle 4.22254 ( 1755) covalent geometry : bond 0.00272 ( 9021) covalent geometry : angle 0.53572 (12225) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.927 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.9373 (ttm) cc_final: 0.9149 (ttm) REVERT: A 141 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6818 (mp0) REVERT: A 686 PHE cc_start: 0.7809 (OUTLIER) cc_final: 0.7457 (t80) REVERT: A 794 GLN cc_start: 0.6980 (mm-40) cc_final: 0.6681 (mt0) REVERT: A 796 GLU cc_start: 0.7804 (pm20) cc_final: 0.7518 (pm20) REVERT: A 1184 MET cc_start: 0.8618 (tpt) cc_final: 0.8323 (tpp) outliers start: 23 outliers final: 14 residues processed: 121 average time/residue: 0.2083 time to fit residues: 35.9653 Evaluate side-chains 118 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 686 PHE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 1058 VAL Chi-restraints excluded: chain A residue 1069 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 28 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 43 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 33 optimal weight: 0.0980 chunk 97 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 GLN A1119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.159108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.106082 restraints weight = 12239.754| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.42 r_work: 0.3118 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9021 Z= 0.212 Angle : 0.598 11.874 12225 Z= 0.318 Chirality : 0.042 0.193 1411 Planarity : 0.004 0.041 1542 Dihedral : 8.293 135.765 1294 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.80 % Allowed : 17.63 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.25), residues: 1140 helix: 1.89 (0.19), residues: 720 sheet: -1.74 (0.77), residues: 49 loop : -1.53 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 441 HIS 0.011 0.002 HIS A1228 PHE 0.017 0.002 PHE A1075 TYR 0.021 0.002 TYR A1093 ARG 0.003 0.000 ARG A1179 Details of bonding type rmsd hydrogen bonds : bond 0.06044 ( 600) hydrogen bonds : angle 4.38384 ( 1755) covalent geometry : bond 0.00492 ( 9021) covalent geometry : angle 0.59842 (12225) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.885 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.9395 (ttm) cc_final: 0.9150 (ttm) REVERT: A 141 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6934 (mp0) REVERT: A 794 GLN cc_start: 0.7019 (mm-40) cc_final: 0.6657 (mt0) REVERT: A 796 GLU cc_start: 0.7855 (pm20) cc_final: 0.7568 (pm20) REVERT: A 1084 MET cc_start: 0.7184 (tpp) cc_final: 0.6622 (tpt) REVERT: A 1184 MET cc_start: 0.8635 (tpt) cc_final: 0.8349 (tpp) outliers start: 26 outliers final: 16 residues processed: 117 average time/residue: 0.1968 time to fit residues: 33.1920 Evaluate side-chains 116 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 1058 VAL Chi-restraints excluded: chain A residue 1069 ILE Chi-restraints excluded: chain A residue 1104 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.0370 chunk 52 optimal weight: 10.0000 chunk 86 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 95 optimal weight: 20.0000 chunk 14 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 108 optimal weight: 9.9990 chunk 88 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 GLN A 451 GLN A 693 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.163742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.112057 restraints weight = 12271.465| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.34 r_work: 0.3192 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9021 Z= 0.126 Angle : 0.551 12.813 12225 Z= 0.288 Chirality : 0.039 0.168 1411 Planarity : 0.004 0.039 1542 Dihedral : 8.003 135.747 1294 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.47 % Allowed : 18.82 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.26), residues: 1140 helix: 2.16 (0.19), residues: 721 sheet: -1.50 (0.79), residues: 47 loop : -1.46 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 441 HIS 0.012 0.001 HIS A1228 PHE 0.012 0.001 PHE A 488 TYR 0.015 0.001 TYR A1093 ARG 0.004 0.000 ARG A 556 Details of bonding type rmsd hydrogen bonds : bond 0.05147 ( 600) hydrogen bonds : angle 4.22598 ( 1755) covalent geometry : bond 0.00253 ( 9021) covalent geometry : angle 0.55059 (12225) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.9349 (ttm) cc_final: 0.8980 (ttm) REVERT: A 141 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6856 (mp0) REVERT: A 477 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7859 (mm-30) REVERT: A 789 MET cc_start: 0.7407 (mmm) cc_final: 0.7001 (mmm) REVERT: A 794 GLN cc_start: 0.6911 (mm-40) cc_final: 0.6650 (mt0) REVERT: A 796 GLU cc_start: 0.7794 (pm20) cc_final: 0.7514 (pm20) REVERT: A 1084 MET cc_start: 0.7219 (tpp) cc_final: 0.6773 (tpt) REVERT: A 1107 GLN cc_start: 0.7485 (mp10) cc_final: 0.7117 (mp10) REVERT: A 1184 MET cc_start: 0.8601 (tpt) cc_final: 0.8263 (tpp) outliers start: 23 outliers final: 19 residues processed: 119 average time/residue: 0.1962 time to fit residues: 33.5433 Evaluate side-chains 120 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 986 PHE Chi-restraints excluded: chain A residue 1058 VAL Chi-restraints excluded: chain A residue 1069 ILE Chi-restraints excluded: chain A residue 1104 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 8 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 GLN A 451 GLN A 693 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.158694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.106874 restraints weight = 12289.254| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.53 r_work: 0.3101 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9021 Z= 0.225 Angle : 0.628 13.418 12225 Z= 0.333 Chirality : 0.043 0.168 1411 Planarity : 0.004 0.041 1542 Dihedral : 8.112 132.625 1294 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.58 % Allowed : 19.78 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.25), residues: 1140 helix: 1.82 (0.19), residues: 721 sheet: -1.68 (0.77), residues: 49 loop : -1.52 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 441 HIS 0.012 0.002 HIS A1228 PHE 0.016 0.002 PHE A1075 TYR 0.019 0.002 TYR A1093 ARG 0.004 0.001 ARG A1091 Details of bonding type rmsd hydrogen bonds : bond 0.06178 ( 600) hydrogen bonds : angle 4.44472 ( 1755) covalent geometry : bond 0.00523 ( 9021) covalent geometry : angle 0.62829 (12225) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.870 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.9345 (ttm) cc_final: 0.8974 (ttm) REVERT: A 141 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6979 (mp0) REVERT: A 477 GLU cc_start: 0.8399 (mm-30) cc_final: 0.7914 (mm-30) REVERT: A 794 GLN cc_start: 0.6832 (mm-40) cc_final: 0.6590 (mt0) REVERT: A 796 GLU cc_start: 0.7905 (pm20) cc_final: 0.7672 (pm20) REVERT: A 986 PHE cc_start: 0.7015 (OUTLIER) cc_final: 0.6680 (m-80) REVERT: A 1029 ILE cc_start: 0.9188 (pt) cc_final: 0.8708 (mp) REVERT: A 1084 MET cc_start: 0.7128 (tpp) cc_final: 0.6770 (tpt) REVERT: A 1184 MET cc_start: 0.8617 (tpt) cc_final: 0.7929 (tpp) outliers start: 24 outliers final: 17 residues processed: 116 average time/residue: 0.1945 time to fit residues: 32.3571 Evaluate side-chains 119 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 693 ASN Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 981 THR Chi-restraints excluded: chain A residue 986 PHE Chi-restraints excluded: chain A residue 1058 VAL Chi-restraints excluded: chain A residue 1069 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 58 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 73 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 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 251 GLN A 451 GLN A 693 ASN ** A1202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.162599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.110930 restraints weight = 12178.664| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.18 r_work: 0.3181 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9021 Z= 0.135 Angle : 0.585 14.254 12225 Z= 0.303 Chirality : 0.040 0.167 1411 Planarity : 0.004 0.044 1542 Dihedral : 7.810 132.873 1294 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.37 % Allowed : 20.11 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.24 (0.25), residues: 1140 helix: 2.07 (0.19), residues: 720 sheet: -1.64 (0.78), residues: 49 loop : -1.41 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 441 HIS 0.013 0.001 HIS A1228 PHE 0.011 0.001 PHE A 488 TYR 0.014 0.001 TYR A1093 ARG 0.004 0.000 ARG A 556 Details of bonding type rmsd hydrogen bonds : bond 0.05379 ( 600) hydrogen bonds : angle 4.32298 ( 1755) covalent geometry : bond 0.00278 ( 9021) covalent geometry : angle 0.58465 (12225) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9340 (ttm) cc_final: 0.8987 (ttm) REVERT: A 141 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6842 (mp0) REVERT: A 477 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7882 (mm-30) REVERT: A 532 GLU cc_start: 0.7132 (mm-30) cc_final: 0.6877 (mm-30) REVERT: A 789 MET cc_start: 0.7394 (mmm) cc_final: 0.7162 (mmm) REVERT: A 794 GLN cc_start: 0.6904 (mm-40) cc_final: 0.6569 (mt0) REVERT: A 796 GLU cc_start: 0.7869 (pm20) cc_final: 0.7646 (pm20) REVERT: A 1007 GLU cc_start: 0.8750 (pt0) cc_final: 0.8508 (pt0) REVERT: A 1029 ILE cc_start: 0.9136 (pt) cc_final: 0.8642 (mp) REVERT: A 1084 MET cc_start: 0.7123 (tpp) cc_final: 0.6799 (tpt) REVERT: A 1184 MET cc_start: 0.8556 (tpt) cc_final: 0.7840 (tpp) outliers start: 22 outliers final: 19 residues processed: 116 average time/residue: 0.2256 time to fit residues: 37.3960 Evaluate side-chains 121 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 2.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 693 ASN Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 986 PHE Chi-restraints excluded: chain A residue 1058 VAL Chi-restraints excluded: chain A residue 1069 ILE Chi-restraints excluded: chain A residue 1111 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 9 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 47 optimal weight: 0.1980 chunk 79 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 chunk 110 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 GLN A 451 GLN A 693 ASN ** A1202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.164540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.111458 restraints weight = 12167.058| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.19 r_work: 0.3198 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9021 Z= 0.126 Angle : 0.576 14.484 12225 Z= 0.296 Chirality : 0.039 0.188 1411 Planarity : 0.004 0.042 1542 Dihedral : 7.436 128.738 1294 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.26 % Allowed : 20.11 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.26), residues: 1140 helix: 2.16 (0.19), residues: 725 sheet: -1.46 (0.79), residues: 47 loop : -1.33 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 441 HIS 0.019 0.001 HIS A1228 PHE 0.009 0.001 PHE A1075 TYR 0.013 0.001 TYR A1093 ARG 0.004 0.000 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.05044 ( 600) hydrogen bonds : angle 4.23498 ( 1755) covalent geometry : bond 0.00251 ( 9021) covalent geometry : angle 0.57581 (12225) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5833.73 seconds wall clock time: 101 minutes 10.45 seconds (6070.45 seconds total)