Starting phenix.real_space_refine on Mon May 12 08:29:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9juo_61832/05_2025/9juo_61832.cif Found real_map, /net/cci-nas-00/data/ceres_data/9juo_61832/05_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_61832/05_2025/9juo_61832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9juo_61832/05_2025/9juo_61832.map" model { file = "/net/cci-nas-00/data/ceres_data/9juo_61832/05_2025/9juo_61832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9juo_61832/05_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-5687/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: 5.50, per 1000 atoms: 0.62 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: 2.46 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: 1.03 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: 2.83 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: 0.000 Normalize map: mean=0, sd=1: 0.890 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.010 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.260 ------------------------------------------------------------------------------- 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 : 0.894 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: 0.2088 time to fit residues: 42.3220 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 : 0.771 ------------------------------------------------------------------------------- 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 = 0.114103 restraints weight = 12001.738| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.48 r_work: 0.3210 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.21 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 : 1.128 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.9356 (ttm) cc_final: 0.9095 (ttm) REVERT: A 780 MET cc_start: 0.9038 (mtp) cc_final: 0.8743 (mtm) REVERT: A 1001 ASP cc_start: 0.7652 (m-30) cc_final: 0.7448 (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: 0.2105 time to fit residues: 33.5024 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 : 1.027 ------------------------------------------------------------------------------- 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: 0.9990 chunk 103 optimal weight: 8.9990 chunk 15 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.3684 ------------------------------------------------------------------------------- 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 = 0.4070 r_free = 0.4070 target = 0.163996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.110826 restraints weight = 12200.555| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.16 r_work: 0.3190 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1569 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= 0.153 Angle : 0.543 8.850 12225 Z= 0.288 Chirality : 0.040 0.140 1411 Planarity : 0.004 0.049 1542 Dihedral : 8.772 142.146 1294 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.37 % Allowed : 11.72 % Favored : 85.91 % 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: 1.25 (0.25), residues: 1140 helix: 2.16 (0.19), residues: 722 sheet: -2.13 (0.72), residues: 49 loop : -1.52 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 441 HIS 0.008 0.002 HIS A1228 PHE 0.011 0.001 PHE A 72 TYR 0.011 0.001 TYR A 89 ARG 0.008 0.000 ARG A1212 Details of bonding type rmsd hydrogen bonds : bond 0.05515 ( 600) hydrogen bonds : angle 4.23372 ( 1755) covalent geometry : bond 0.00335 ( 9021) covalent geometry : angle 0.54321 (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 130 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.921 Fit side-chains REVERT: A 801 ARG cc_start: 0.7470 (ttp-170) cc_final: 0.7171 (ttm110) REVERT: A 1084 MET cc_start: 0.7188 (tpp) cc_final: 0.6950 (tpt) outliers start: 22 outliers final: 11 residues processed: 121 average time/residue: 0.1876 time to fit residues: 32.5892 Evaluate side-chains 111 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.885 ------------------------------------------------------------------------------- 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 686 PHE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 813 VAL 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: 0.6980 chunk 109 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 96 optimal weight: 0.1980 chunk 103 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 68 optimal weight: 0.0870 overall best weight: 0.9962 ------------------------------------------------------------------------------- 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 = 0.4081 r_free = 0.4081 target = 0.165095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.111963 restraints weight = 12032.961| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.40 r_work: 0.3195 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9021 Z= 0.131 Angle : 0.516 9.268 12225 Z= 0.275 Chirality : 0.039 0.133 1411 Planarity : 0.004 0.041 1542 Dihedral : 8.311 140.573 1294 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.94 % Allowed : 14.19 % Favored : 83.87 % 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: 1.35 (0.25), residues: 1140 helix: 2.24 (0.19), residues: 721 sheet: -2.00 (0.72), residues: 49 loop : -1.49 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 441 HIS 0.008 0.001 HIS A1228 PHE 0.008 0.001 PHE A 72 TYR 0.009 0.001 TYR A 89 ARG 0.005 0.000 ARG A1212 Details of bonding type rmsd hydrogen bonds : bond 0.05184 ( 600) hydrogen bonds : angle 4.17180 ( 1755) covalent geometry : bond 0.00274 ( 9021) covalent geometry : angle 0.51558 (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 123 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.910 Fit side-chains REVERT: A 122 MET cc_start: 0.9394 (ttm) cc_final: 0.9047 (ttm) REVERT: A 141 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6816 (mp0) REVERT: A 686 PHE cc_start: 0.7836 (OUTLIER) cc_final: 0.7463 (t80) REVERT: A 801 ARG cc_start: 0.7538 (ttp-170) cc_final: 0.7195 (ttm110) REVERT: A 986 PHE cc_start: 0.7356 (m-80) cc_final: 0.7129 (m-80) outliers start: 18 outliers final: 12 residues processed: 114 average time/residue: 0.1967 time to fit residues: 32.0916 Evaluate side-chains 115 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 35 optimal weight: 7.9990 chunk 87 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 96 optimal weight: 0.0270 chunk 57 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 overall best weight: 1.0842 ------------------------------------------------------------------------------- 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 = 0.4075 r_free = 0.4075 target = 0.163338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.111448 restraints weight = 12143.289| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.56 r_work: 0.3184 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1893 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= 0.135 Angle : 0.517 9.480 12225 Z= 0.275 Chirality : 0.039 0.129 1411 Planarity : 0.004 0.038 1542 Dihedral : 8.142 138.910 1294 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.47 % Allowed : 14.84 % Favored : 82.69 % 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: 1.37 (0.25), residues: 1140 helix: 2.25 (0.19), residues: 719 sheet: -1.90 (0.73), residues: 49 loop : -1.49 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 441 HIS 0.009 0.001 HIS A1228 PHE 0.012 0.001 PHE A1075 TYR 0.010 0.001 TYR A 89 ARG 0.003 0.000 ARG A1212 Details of bonding type rmsd hydrogen bonds : bond 0.05185 ( 600) hydrogen bonds : angle 4.14262 ( 1755) covalent geometry : bond 0.00287 ( 9021) covalent geometry : angle 0.51704 (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 125 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.868 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.9393 (ttm) cc_final: 0.9098 (ttm) REVERT: A 141 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6877 (mp0) REVERT: A 686 PHE cc_start: 0.7817 (OUTLIER) cc_final: 0.7479 (t80) REVERT: A 794 GLN cc_start: 0.6898 (mm-40) cc_final: 0.6549 (mt0) REVERT: A 796 GLU cc_start: 0.7814 (pm20) cc_final: 0.7515 (pm20) outliers start: 23 outliers final: 14 residues processed: 115 average time/residue: 0.1928 time to fit residues: 31.9728 Evaluate side-chains 115 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 65 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 11 optimal weight: 0.0030 chunk 108 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 1 optimal weight: 0.4980 chunk 3 optimal weight: 3.9990 overall best weight: 1.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.163365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.111235 restraints weight = 12201.139| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.36 r_work: 0.3191 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1975 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= 0.136 Angle : 0.528 10.600 12225 Z= 0.281 Chirality : 0.039 0.154 1411 Planarity : 0.004 0.037 1542 Dihedral : 8.043 137.835 1294 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.58 % Allowed : 15.81 % 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: 1.36 (0.25), residues: 1140 helix: 2.23 (0.19), residues: 719 sheet: -1.79 (0.75), residues: 49 loop : -1.48 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 441 HIS 0.010 0.001 HIS A1228 PHE 0.013 0.001 PHE A 488 TYR 0.016 0.001 TYR A1093 ARG 0.002 0.000 ARG A1212 Details of bonding type rmsd hydrogen bonds : bond 0.05156 ( 600) hydrogen bonds : angle 4.15669 ( 1755) covalent geometry : bond 0.00291 ( 9021) covalent geometry : angle 0.52758 (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 128 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.989 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.9382 (ttm) cc_final: 0.9085 (ttm) REVERT: A 141 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6832 (mp0) REVERT: A 216 SER cc_start: 0.8812 (t) cc_final: 0.8536 (p) REVERT: A 686 PHE cc_start: 0.7804 (OUTLIER) cc_final: 0.7444 (t80) REVERT: A 794 GLN cc_start: 0.6948 (mm-40) cc_final: 0.6697 (mt0) REVERT: A 796 GLU cc_start: 0.7770 (pm20) cc_final: 0.7467 (pm20) REVERT: A 986 PHE cc_start: 0.6929 (OUTLIER) cc_final: 0.6646 (t80) REVERT: A 1107 GLN cc_start: 0.7617 (mp10) cc_final: 0.7249 (mp10) REVERT: A 1184 MET cc_start: 0.8629 (tpt) cc_final: 0.8350 (tpp) outliers start: 24 outliers final: 16 residues processed: 116 average time/residue: 0.1927 time to fit residues: 32.1434 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 : 0.960 ------------------------------------------------------------------------------- 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 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 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 986 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: 3.9990 chunk 51 optimal weight: 1.9990 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: 6.9990 chunk 53 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 97 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.160409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.107941 restraints weight = 12198.222| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.36 r_work: 0.3139 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2143 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= 0.184 Angle : 0.576 10.876 12225 Z= 0.305 Chirality : 0.041 0.199 1411 Planarity : 0.004 0.037 1542 Dihedral : 8.111 135.551 1294 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.69 % Allowed : 16.34 % Favored : 80.97 % 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: 1.13 (0.25), residues: 1140 helix: 2.01 (0.19), residues: 718 sheet: -1.73 (0.76), residues: 49 loop : -1.49 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 441 HIS 0.010 0.002 HIS A1228 PHE 0.016 0.001 PHE A1075 TYR 0.019 0.002 TYR A1093 ARG 0.003 0.000 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.05773 ( 600) hydrogen bonds : angle 4.30750 ( 1755) covalent geometry : bond 0.00420 ( 9021) covalent geometry : angle 0.57595 (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 125 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.904 Fit side-chains revert: symmetry clash REVERT: A 141 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6866 (mp0) REVERT: A 794 GLN cc_start: 0.6935 (mm-40) cc_final: 0.6562 (mt0) REVERT: A 796 GLU cc_start: 0.7810 (pm20) cc_final: 0.7504 (pm20) REVERT: A 1084 MET cc_start: 0.7187 (tpp) cc_final: 0.6600 (tpt) REVERT: A 1184 MET cc_start: 0.8635 (tpt) cc_final: 0.8355 (tpp) outliers start: 25 outliers final: 17 residues processed: 114 average time/residue: 0.2022 time to fit residues: 33.0430 Evaluate side-chains 116 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 95 optimal weight: 20.0000 chunk 14 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 108 optimal weight: 9.9990 chunk 88 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 A1119 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 = 0.163773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.112352 restraints weight = 12270.238| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.37 r_work: 0.3190 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9021 Z= 0.130 Angle : 0.555 12.826 12225 Z= 0.286 Chirality : 0.039 0.177 1411 Planarity : 0.004 0.037 1542 Dihedral : 7.764 134.229 1294 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.69 % Allowed : 16.77 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.26), residues: 1140 helix: 2.19 (0.19), residues: 720 sheet: -1.71 (0.76), residues: 49 loop : -1.43 (0.31), residues: 371 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 0.003 0.000 ARG A 556 Details of bonding type rmsd hydrogen bonds : bond 0.05174 ( 600) hydrogen bonds : angle 4.21089 ( 1755) covalent geometry : bond 0.00269 ( 9021) covalent geometry : angle 0.55535 (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: 25 poor density : 103 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.9378 (ttm) cc_final: 0.9094 (ttm) REVERT: A 141 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6838 (mp0) REVERT: A 477 GLU cc_start: 0.8387 (mm-30) cc_final: 0.7894 (mm-30) REVERT: A 789 MET cc_start: 0.7428 (mmm) cc_final: 0.7012 (mmm) REVERT: A 794 GLN cc_start: 0.6945 (mm-40) cc_final: 0.6627 (mt0) REVERT: A 796 GLU cc_start: 0.7729 (pm20) cc_final: 0.7433 (pm20) REVERT: A 1084 MET cc_start: 0.7195 (tpp) cc_final: 0.6735 (tpt) REVERT: A 1107 GLN cc_start: 0.7497 (mp10) cc_final: 0.7114 (mp10) REVERT: A 1184 MET cc_start: 0.8611 (tpt) cc_final: 0.8275 (tpp) outliers start: 25 outliers final: 18 residues processed: 117 average time/residue: 0.1937 time to fit residues: 32.4670 Evaluate side-chains 118 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 8 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 1 optimal weight: 0.1980 chunk 98 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.161856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.109728 restraints weight = 12239.184| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.22 r_work: 0.3167 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9021 Z= 0.166 Angle : 0.585 12.390 12225 Z= 0.304 Chirality : 0.041 0.182 1411 Planarity : 0.004 0.041 1542 Dihedral : 7.650 130.505 1294 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.37 % Allowed : 17.53 % Favored : 80.11 % 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: 1.22 (0.25), residues: 1140 helix: 2.06 (0.19), residues: 721 sheet: -1.69 (0.77), residues: 49 loop : -1.43 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 441 HIS 0.013 0.002 HIS A1228 PHE 0.016 0.001 PHE A1075 TYR 0.016 0.001 TYR A1093 ARG 0.010 0.000 ARG A1212 Details of bonding type rmsd hydrogen bonds : bond 0.05539 ( 600) hydrogen bonds : angle 4.27917 ( 1755) covalent geometry : bond 0.00371 ( 9021) covalent geometry : angle 0.58504 (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 124 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9403 (ttm) cc_final: 0.9164 (ttm) REVERT: A 141 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6832 (mp0) REVERT: A 477 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7861 (mm-30) REVERT: A 789 MET cc_start: 0.7268 (mmm) cc_final: 0.7004 (tpp) REVERT: A 794 GLN cc_start: 0.6951 (mm-40) cc_final: 0.6614 (mt0) REVERT: A 796 GLU cc_start: 0.7723 (pm20) cc_final: 0.7427 (pm20) REVERT: A 1084 MET cc_start: 0.7104 (tpp) cc_final: 0.6749 (tpt) REVERT: A 1184 MET cc_start: 0.8552 (tpt) cc_final: 0.7844 (tpp) outliers start: 22 outliers final: 19 residues processed: 114 average time/residue: 0.1934 time to fit residues: 32.0094 Evaluate side-chains 117 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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 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 867 MET 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: 2.9990 chunk 39 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 73 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 55 optimal weight: 20.0000 chunk 16 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.163644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.111986 restraints weight = 12188.696| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.40 r_work: 0.3182 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9021 Z= 0.137 Angle : 0.574 13.671 12225 Z= 0.296 Chirality : 0.040 0.193 1411 Planarity : 0.004 0.042 1542 Dihedral : 7.359 127.159 1294 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.15 % Allowed : 17.96 % Favored : 79.89 % 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: 1.36 (0.26), residues: 1140 helix: 2.20 (0.19), residues: 719 sheet: -1.62 (0.78), residues: 49 loop : -1.42 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 441 HIS 0.017 0.001 HIS A1228 PHE 0.014 0.001 PHE A1075 TYR 0.014 0.001 TYR A1093 ARG 0.012 0.000 ARG A1212 Details of bonding type rmsd hydrogen bonds : bond 0.05193 ( 600) hydrogen bonds : angle 4.23434 ( 1755) covalent geometry : bond 0.00289 ( 9021) covalent geometry : angle 0.57391 (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 122 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9375 (ttm) cc_final: 0.9091 (ttm) REVERT: A 141 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6805 (mp0) REVERT: A 477 GLU cc_start: 0.8376 (mm-30) cc_final: 0.7866 (mm-30) REVERT: A 789 MET cc_start: 0.7256 (mmm) cc_final: 0.7007 (tpp) REVERT: A 794 GLN cc_start: 0.6922 (mm-40) cc_final: 0.6710 (mt0) REVERT: A 796 GLU cc_start: 0.7684 (pm20) cc_final: 0.7373 (pm20) REVERT: A 1084 MET cc_start: 0.7100 (tpp) cc_final: 0.6757 (tpt) REVERT: A 1184 MET cc_start: 0.8580 (tpt) cc_final: 0.7870 (tpp) outliers start: 20 outliers final: 18 residues processed: 113 average time/residue: 0.1999 time to fit residues: 32.2983 Evaluate side-chains 121 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 1.410 ------------------------------------------------------------------------------- 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 359 VAL 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 530 LEU Chi-restraints excluded: chain A residue 554 ILE 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 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 9 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.163475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.109615 restraints weight = 12160.412| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.20 r_work: 0.3180 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2310 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= 0.141 Angle : 0.578 14.055 12225 Z= 0.296 Chirality : 0.040 0.182 1411 Planarity : 0.004 0.041 1542 Dihedral : 7.193 122.545 1294 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.15 % Allowed : 18.17 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.36 (0.26), residues: 1140 helix: 2.17 (0.19), residues: 720 sheet: -1.41 (0.80), residues: 47 loop : -1.39 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 441 HIS 0.015 0.001 HIS A1228 PHE 0.014 0.001 PHE A1075 TYR 0.014 0.001 TYR A1093 ARG 0.012 0.000 ARG A1212 Details of bonding type rmsd hydrogen bonds : bond 0.05226 ( 600) hydrogen bonds : angle 4.21396 ( 1755) covalent geometry : bond 0.00303 ( 9021) covalent geometry : angle 0.57760 (12225) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5454.29 seconds wall clock time: 94 minutes 52.13 seconds (5692.13 seconds total)