Starting phenix.real_space_refine on Wed Sep 17 13:17:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9juo_61832/09_2025/9juo_61832.cif Found real_map, /net/cci-nas-00/data/ceres_data/9juo_61832/09_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_61832/09_2025/9juo_61832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9juo_61832/09_2025/9juo_61832.map" model { file = "/net/cci-nas-00/data/ceres_data/9juo_61832/09_2025/9juo_61832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9juo_61832/09_2025/9juo_61832.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.24, per 1000 atoms: 0.25 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: 0.98 Conformation dependent library (CDL) restraints added in 339.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.28 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: 1.40 Time building geometry restraints manager: 1.25 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: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 9.700 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.350 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG A1099 TYR 0.015 0.001 TYR A1093 PHE 0.024 0.001 PHE A 686 TRP 0.008 0.001 TRP A 188 HIS 0.003 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00532 ( 9021) covalent geometry : angle 0.69881 (12225) hydrogen bonds : bond 0.12698 ( 600) hydrogen bonds : angle 5.37283 ( 1755) *********************** 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 : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 SER cc_start: 0.8755 (t) cc_final: 0.8516 (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: 0.0941 time to fit residues: 19.2572 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 : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 30.0000 chunk 100 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 A 842 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.158800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.104942 restraints weight = 12357.616| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.66 r_work: 0.3087 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 9021 Z= 0.303 Angle : 0.687 10.409 12225 Z= 0.364 Chirality : 0.046 0.184 1411 Planarity : 0.005 0.072 1542 Dihedral : 10.838 138.635 1294 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.26 % Allowed : 11.18 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.25), residues: 1140 helix: 1.63 (0.19), residues: 720 sheet: -2.10 (0.71), residues: 49 loop : -1.66 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1099 TYR 0.018 0.002 TYR A1093 PHE 0.020 0.002 PHE A 72 TRP 0.020 0.003 TRP A 441 HIS 0.011 0.002 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00710 ( 9021) covalent geometry : angle 0.68667 (12225) hydrogen bonds : bond 0.06926 ( 600) hydrogen bonds : angle 4.65966 ( 1755) *********************** 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: 21 poor density : 95 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9378 (ttm) cc_final: 0.9058 (ttm) REVERT: A 1084 MET cc_start: 0.7382 (tpp) cc_final: 0.7042 (tpt) outliers start: 21 outliers final: 12 residues processed: 108 average time/residue: 0.0853 time to fit residues: 13.1854 Evaluate side-chains 104 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.209 ------------------------------------------------------------------------------- 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 768 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 819 ASP Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 1069 ILE Chi-restraints excluded: chain A residue 1071 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 7 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 80 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 GLN A 445 GLN A 451 GLN A 771 ASN A1142 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.163915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.109910 restraints weight = 12146.058| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.42 r_work: 0.3163 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9021 Z= 0.131 Angle : 0.535 9.933 12225 Z= 0.281 Chirality : 0.039 0.131 1411 Planarity : 0.004 0.051 1542 Dihedral : 9.041 143.467 1294 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.83 % Allowed : 14.41 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.25), residues: 1140 helix: 2.04 (0.19), residues: 720 sheet: -1.99 (0.72), residues: 49 loop : -1.55 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1179 TYR 0.010 0.001 TYR A1093 PHE 0.009 0.001 PHE A 866 TRP 0.015 0.001 TRP A 441 HIS 0.005 0.001 HIS A 486 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 9021) covalent geometry : angle 0.53494 (12225) hydrogen bonds : bond 0.05424 ( 600) hydrogen bonds : angle 4.29869 ( 1755) *********************** 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 124 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.9364 (ttm) cc_final: 0.9081 (ttm) REVERT: A 986 PHE cc_start: 0.7317 (m-80) cc_final: 0.7019 (m-80) REVERT: A 1084 MET cc_start: 0.7188 (tpp) cc_final: 0.6941 (tpt) outliers start: 17 outliers final: 11 residues processed: 117 average time/residue: 0.0894 time to fit residues: 14.9348 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 : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 SER 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 806 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 832 LEU 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 15 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 91 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 21 optimal weight: 0.5980 chunk 57 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- 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 A 693 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.158491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.103385 restraints weight = 12455.914| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.63 r_work: 0.3070 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 9021 Z= 0.263 Angle : 0.626 9.895 12225 Z= 0.336 Chirality : 0.043 0.154 1411 Planarity : 0.004 0.048 1542 Dihedral : 8.868 141.525 1294 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.90 % Allowed : 16.56 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.25), residues: 1140 helix: 1.68 (0.19), residues: 720 sheet: -1.90 (0.74), residues: 49 loop : -1.61 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1212 TYR 0.015 0.002 TYR A 89 PHE 0.015 0.002 PHE A 33 TRP 0.013 0.002 TRP A 441 HIS 0.010 0.002 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00617 ( 9021) covalent geometry : angle 0.62586 (12225) hydrogen bonds : bond 0.06559 ( 600) hydrogen bonds : angle 4.51209 ( 1755) *********************** 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 127 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.9409 (ttm) cc_final: 0.9081 (ttm) REVERT: A 141 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6981 (mp0) REVERT: A 484 ASN cc_start: 0.8564 (t0) cc_final: 0.8343 (t0) REVERT: A 1084 MET cc_start: 0.7097 (tpp) cc_final: 0.6876 (tpt) outliers start: 27 outliers final: 20 residues processed: 117 average time/residue: 0.0827 time to fit residues: 14.0349 Evaluate side-chains 119 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 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 768 VAL Chi-restraints excluded: chain A residue 788 GLU 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 Chi-restraints excluded: chain A residue 1104 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 68 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 52 optimal weight: 0.0970 chunk 110 optimal weight: 9.9990 chunk 22 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 95 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.160081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.107857 restraints weight = 12244.109| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.45 r_work: 0.3128 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9021 Z= 0.162 Angle : 0.560 10.099 12225 Z= 0.299 Chirality : 0.040 0.148 1411 Planarity : 0.004 0.043 1542 Dihedral : 8.602 143.561 1294 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.15 % Allowed : 17.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.25), residues: 1140 helix: 1.82 (0.19), residues: 726 sheet: -1.78 (0.75), residues: 49 loop : -1.57 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1212 TYR 0.019 0.001 TYR A1093 PHE 0.009 0.001 PHE A 866 TRP 0.014 0.001 TRP A 441 HIS 0.006 0.001 HIS A1228 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 9021) covalent geometry : angle 0.55955 (12225) hydrogen bonds : bond 0.05732 ( 600) hydrogen bonds : angle 4.37215 ( 1755) *********************** 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 122 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 141 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6939 (mp0) REVERT: A 484 ASN cc_start: 0.8630 (t0) cc_final: 0.8427 (t0) REVERT: A 789 MET cc_start: 0.7591 (mmm) cc_final: 0.7252 (mmm) REVERT: A 986 PHE cc_start: 0.7462 (m-80) cc_final: 0.7152 (m-80) REVERT: A 1084 MET cc_start: 0.7081 (tpp) cc_final: 0.6836 (tpp) outliers start: 20 outliers final: 15 residues processed: 112 average time/residue: 0.0718 time to fit residues: 11.9082 Evaluate side-chains 112 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.277 ------------------------------------------------------------------------------- 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 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 1058 VAL Chi-restraints excluded: chain A residue 1069 ILE Chi-restraints excluded: chain A residue 1104 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 38 optimal weight: 20.0000 chunk 85 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.4053 r_free = 0.4053 target = 0.161552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.109233 restraints weight = 12197.085| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.35 r_work: 0.3163 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2197 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= 0.138 Angle : 0.540 10.515 12225 Z= 0.284 Chirality : 0.039 0.144 1411 Planarity : 0.004 0.038 1542 Dihedral : 8.379 145.353 1294 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.37 % Allowed : 17.63 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.25), residues: 1140 helix: 2.00 (0.19), residues: 725 sheet: -1.74 (0.75), residues: 49 loop : -1.52 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1212 TYR 0.016 0.001 TYR A1093 PHE 0.011 0.001 PHE A 488 TRP 0.015 0.001 TRP A 441 HIS 0.008 0.001 HIS A1228 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 9021) covalent geometry : angle 0.53994 (12225) hydrogen bonds : bond 0.05334 ( 600) hydrogen bonds : angle 4.24421 ( 1755) *********************** 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 125 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6831 (mp0) REVERT: A 686 PHE cc_start: 0.7816 (OUTLIER) cc_final: 0.7462 (t80) REVERT: A 794 GLN cc_start: 0.7001 (mm-40) cc_final: 0.6781 (mt0) REVERT: A 796 GLU cc_start: 0.7850 (pm20) cc_final: 0.7553 (pm20) REVERT: A 1084 MET cc_start: 0.7035 (tpp) cc_final: 0.6811 (tpp) outliers start: 22 outliers final: 17 residues processed: 116 average time/residue: 0.0815 time to fit residues: 13.8508 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 : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL 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 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 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 1104 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 86 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 109 optimal weight: 0.7980 chunk 99 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 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 = 0.4068 r_free = 0.4068 target = 0.162698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.111681 restraints weight = 12227.874| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.32 r_work: 0.3179 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2223 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= 0.131 Angle : 0.534 11.988 12225 Z= 0.279 Chirality : 0.039 0.169 1411 Planarity : 0.004 0.036 1542 Dihedral : 8.233 145.756 1294 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.58 % Allowed : 18.82 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.25), residues: 1140 helix: 2.10 (0.19), residues: 720 sheet: -1.73 (0.76), residues: 49 loop : -1.49 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1212 TYR 0.014 0.001 TYR A1093 PHE 0.009 0.001 PHE A 866 TRP 0.017 0.001 TRP A 441 HIS 0.010 0.001 HIS A1228 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 9021) covalent geometry : angle 0.53387 (12225) hydrogen bonds : bond 0.05196 ( 600) hydrogen bonds : angle 4.21041 ( 1755) *********************** 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 131 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9357 (ttm) cc_final: 0.9099 (ttm) REVERT: A 141 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6826 (mp0) REVERT: A 686 PHE cc_start: 0.7771 (OUTLIER) cc_final: 0.7465 (t80) REVERT: A 796 GLU cc_start: 0.7826 (pm20) cc_final: 0.7527 (pm20) REVERT: A 1084 MET cc_start: 0.7002 (tpp) cc_final: 0.6718 (tpt) outliers start: 24 outliers final: 19 residues processed: 120 average time/residue: 0.0797 time to fit residues: 14.0546 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 : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 120 THR 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 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 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 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 3 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 76 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 GLN A 513 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.162908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.111059 restraints weight = 12161.304| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.16 r_work: 0.3178 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 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 0.032 9021 Z= 0.134 Angle : 0.541 13.066 12225 Z= 0.281 Chirality : 0.039 0.182 1411 Planarity : 0.004 0.036 1542 Dihedral : 8.124 146.124 1294 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.80 % Allowed : 19.25 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.25), residues: 1140 helix: 2.11 (0.19), residues: 720 sheet: -1.56 (0.78), residues: 47 loop : -1.45 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1212 TYR 0.013 0.001 TYR A1093 PHE 0.011 0.001 PHE A 488 TRP 0.017 0.001 TRP A 441 HIS 0.015 0.001 HIS A1228 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9021) covalent geometry : angle 0.54113 (12225) hydrogen bonds : bond 0.05194 ( 600) hydrogen bonds : angle 4.19395 ( 1755) *********************** 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 126 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9335 (ttm) cc_final: 0.9060 (ttm) REVERT: A 141 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6815 (mp0) REVERT: A 686 PHE cc_start: 0.7752 (OUTLIER) cc_final: 0.7465 (t80) REVERT: A 1084 MET cc_start: 0.6983 (tpp) cc_final: 0.6711 (tpt) outliers start: 26 outliers final: 20 residues processed: 114 average time/residue: 0.0756 time to fit residues: 12.5907 Evaluate side-chains 119 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 120 THR 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 273 MET 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 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 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 100 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 111 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.159353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.105028 restraints weight = 12252.632| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.25 r_work: 0.3110 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9021 Z= 0.204 Angle : 0.596 13.537 12225 Z= 0.313 Chirality : 0.042 0.183 1411 Planarity : 0.004 0.040 1542 Dihedral : 8.272 146.502 1294 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.58 % Allowed : 20.11 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.25), residues: 1140 helix: 1.86 (0.19), residues: 720 sheet: -1.71 (0.77), residues: 49 loop : -1.45 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1212 TYR 0.016 0.002 TYR A1093 PHE 0.011 0.001 PHE A 33 TRP 0.014 0.002 TRP A 441 HIS 0.014 0.002 HIS A1228 Details of bonding type rmsd covalent geometry : bond 0.00473 ( 9021) covalent geometry : angle 0.59575 (12225) hydrogen bonds : bond 0.05955 ( 600) hydrogen bonds : angle 4.36886 ( 1755) *********************** 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 123 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6934 (mp0) REVERT: A 1029 ILE cc_start: 0.9201 (pt) cc_final: 0.8730 (mp) REVERT: A 1084 MET cc_start: 0.6971 (tpp) cc_final: 0.6689 (tpt) outliers start: 24 outliers final: 18 residues processed: 112 average time/residue: 0.0708 time to fit residues: 11.7597 Evaluate side-chains 115 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 120 THR 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 273 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 45 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 111 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 55 optimal weight: 20.0000 chunk 97 optimal weight: 8.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.159868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.108596 restraints weight = 12193.099| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.56 r_work: 0.3122 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9021 Z= 0.173 Angle : 0.586 14.087 12225 Z= 0.303 Chirality : 0.041 0.184 1411 Planarity : 0.004 0.041 1542 Dihedral : 8.271 149.578 1294 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.58 % Allowed : 20.32 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.25), residues: 1140 helix: 1.86 (0.19), residues: 726 sheet: -1.68 (0.77), residues: 49 loop : -1.42 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 298 TYR 0.015 0.001 TYR A1093 PHE 0.009 0.001 PHE A 488 TRP 0.015 0.001 TRP A 441 HIS 0.015 0.002 HIS A1228 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 9021) covalent geometry : angle 0.58561 (12225) hydrogen bonds : bond 0.05712 ( 600) hydrogen bonds : angle 4.34274 ( 1755) ********************** 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 126 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6898 (mp0) REVERT: A 1007 GLU cc_start: 0.8725 (pt0) cc_final: 0.8507 (pt0) REVERT: A 1029 ILE cc_start: 0.9192 (pt) cc_final: 0.8719 (mp) REVERT: A 1084 MET cc_start: 0.6984 (tpp) cc_final: 0.6705 (tpt) outliers start: 24 outliers final: 23 residues processed: 116 average time/residue: 0.0690 time to fit residues: 11.9074 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 : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 273 MET Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 391 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 49 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 53 optimal weight: 0.0980 chunk 98 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 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 = 0.4054 r_free = 0.4054 target = 0.161609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.107842 restraints weight = 12093.103| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.22 r_work: 0.3149 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9021 Z= 0.143 Angle : 0.568 14.190 12225 Z= 0.292 Chirality : 0.039 0.171 1411 Planarity : 0.004 0.041 1542 Dihedral : 8.217 150.918 1294 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.47 % Allowed : 20.75 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.26), residues: 1140 helix: 1.98 (0.19), residues: 726 sheet: -1.67 (0.77), residues: 49 loop : -1.37 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1212 TYR 0.013 0.001 TYR A1093 PHE 0.009 0.001 PHE A 866 TRP 0.017 0.001 TRP A 441 HIS 0.012 0.001 HIS A1228 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 9021) covalent geometry : angle 0.56762 (12225) hydrogen bonds : bond 0.05420 ( 600) hydrogen bonds : angle 4.28427 ( 1755) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2609.55 seconds wall clock time: 45 minutes 16.62 seconds (2716.62 seconds total)