Starting phenix.real_space_refine on Thu Jul 2 00:36:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yfw_72909/07_2026/9yfw_72909.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yfw_72909/07_2026/9yfw_72909.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9yfw_72909/07_2026/9yfw_72909.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yfw_72909/07_2026/9yfw_72909.map" model { file = "/net/cci-nas-00/data/ceres_data/9yfw_72909/07_2026/9yfw_72909.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yfw_72909/07_2026/9yfw_72909.cif" } resolution = 3.21 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 2909 2.51 5 N 714 2.21 5 O 849 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4500 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 4500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4500 Classifications: {'peptide': 564} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 544} Chain breaks: 4 Time building chain proxies: 1.22, per 1000 atoms: 0.27 Number of scatterers: 4500 At special positions: 0 Unit cell: (81.536, 97.344, 101.504, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 849 8.00 N 714 7.00 C 2909 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: 0.25 Conformation dependent library (CDL) restraints added in 163.4 milliseconds 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1098 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 1 sheets defined 15.6% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'B' and resid 1000 through 1014 removed outlier: 3.502A pdb=" N LEU B1014 " --> pdb=" O LEU B1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1141 removed outlier: 3.761A pdb=" N THR B1140 " --> pdb=" O SER B1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 1161 through 1191 removed outlier: 3.734A pdb=" N LEU B1165 " --> pdb=" O VAL B1161 " (cutoff:3.500A) Processing helix chain 'B' and resid 1325 through 1338 Processing helix chain 'B' and resid 1422 through 1424 No H-bonds generated for 'chain 'B' and resid 1422 through 1424' Processing helix chain 'B' and resid 1510 through 1529 removed outlier: 3.773A pdb=" N PHE B1521 " --> pdb=" O VAL B1517 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 881 through 884 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 881 through 884 current: chain 'B' and resid 904 through 913 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 904 through 913 current: chain 'B' and resid 923 through 930 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 923 through 930 current: chain 'B' and resid 947 through 952 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 947 through 952 current: chain 'B' and resid 985 through 990 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 985 through 990 current: chain 'B' and resid 1052 through 1066 removed outlier: 3.575A pdb=" N LEU B1052 " --> pdb=" O MET B1086 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N CYS B1060 " --> pdb=" O GLU B1078 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLU B1078 " --> pdb=" O CYS B1060 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLN B1062 " --> pdb=" O LYS B1076 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LYS B1076 " --> pdb=" O GLN B1062 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N PHE B1064 " --> pdb=" O GLU B1074 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLU B1074 " --> pdb=" O PHE B1064 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1090 through 1097 current: chain 'B' and resid 1113 through 1117 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1113 through 1117 current: chain 'B' and resid 1147 through 1153 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1147 through 1153 current: chain 'B' and resid 1228 through 1233 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1228 through 1233 current: chain 'B' and resid 1256 through 1265 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1256 through 1265 current: chain 'B' and resid 1278 through 1279 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1278 through 1279 current: chain 'B' and resid 1310 through 1316 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1310 through 1316 current: chain 'B' and resid 1392 through 1408 removed outlier: 5.578A pdb=" N THR B1393 " --> pdb=" O TYR B1442 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N TYR B1442 " --> pdb=" O THR B1393 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ASN B1395 " --> pdb=" O LYS B1440 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LYS B1440 " --> pdb=" O ASN B1395 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N SER B1397 " --> pdb=" O THR B1438 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR B1438 " --> pdb=" O SER B1397 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LYS B1399 " --> pdb=" O ILE B1436 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ILE B1436 " --> pdb=" O LYS B1399 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASP B1401 " --> pdb=" O ASN B1434 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA B1428 " --> pdb=" O LEU B1407 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1447 through 1453 current: chain 'B' and resid 1471 through 1475 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1471 through 1475 current: chain 'B' and resid 1496 through 1500 87 hydrogen bonds defined for protein. 258 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: 0.61 Time building geometry restraints manager: 0.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1421 1.34 - 1.46: 784 1.46 - 1.57: 2326 1.57 - 1.69: 0 1.69 - 1.81: 46 Bond restraints: 4577 Sorted by residual: bond pdb=" N ASN B 956 " pdb=" CA ASN B 956 " ideal model delta sigma weight residual 1.454 1.490 -0.035 1.33e-02 5.65e+03 6.94e+00 bond pdb=" N ASP B 960 " pdb=" CA ASP B 960 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.27e-02 6.20e+03 6.86e+00 bond pdb=" N GLU B 959 " pdb=" CA GLU B 959 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.55e+00 bond pdb=" N MET B 958 " pdb=" CA MET B 958 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.15e-02 7.56e+03 5.47e+00 bond pdb=" N ASP B 955 " pdb=" CA ASP B 955 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.40e-02 5.10e+03 5.30e+00 ... (remaining 4572 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 6107 2.14 - 4.28: 86 4.28 - 6.42: 9 6.42 - 8.56: 3 8.56 - 10.70: 1 Bond angle restraints: 6206 Sorted by residual: angle pdb=" N ASP B 955 " pdb=" CA ASP B 955 " pdb=" C ASP B 955 " ideal model delta sigma weight residual 113.15 107.67 5.48 1.19e+00 7.06e-01 2.12e+01 angle pdb=" CA GLU B1512 " pdb=" CB GLU B1512 " pdb=" CG GLU B1512 " ideal model delta sigma weight residual 114.10 120.83 -6.73 2.00e+00 2.50e-01 1.13e+01 angle pdb=" N ILE B1072 " pdb=" CA ILE B1072 " pdb=" C ILE B1072 " ideal model delta sigma weight residual 111.56 108.92 2.64 8.60e-01 1.35e+00 9.40e+00 angle pdb=" CA LEU B1388 " pdb=" CB LEU B1388 " pdb=" CG LEU B1388 " ideal model delta sigma weight residual 116.30 127.00 -10.70 3.50e+00 8.16e-02 9.35e+00 angle pdb=" CA THR B 957 " pdb=" CB THR B 957 " pdb=" OG1 THR B 957 " ideal model delta sigma weight residual 109.60 105.06 4.54 1.50e+00 4.44e-01 9.15e+00 ... (remaining 6201 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.49: 2351 14.49 - 28.98: 315 28.98 - 43.46: 87 43.46 - 57.95: 31 57.95 - 72.44: 7 Dihedral angle restraints: 2791 sinusoidal: 1113 harmonic: 1678 Sorted by residual: dihedral pdb=" CG ARG B 920 " pdb=" CD ARG B 920 " pdb=" NE ARG B 920 " pdb=" CZ ARG B 920 " ideal model delta sinusoidal sigma weight residual 180.00 138.02 41.98 2 1.50e+01 4.44e-03 9.54e+00 dihedral pdb=" CA GLU B1281 " pdb=" CB GLU B1281 " pdb=" CG GLU B1281 " pdb=" CD GLU B1281 " ideal model delta sinusoidal sigma weight residual 60.00 113.66 -53.66 3 1.50e+01 4.44e-03 9.22e+00 dihedral pdb=" CG LYS B1112 " pdb=" CD LYS B1112 " pdb=" CE LYS B1112 " pdb=" NZ LYS B1112 " ideal model delta sinusoidal sigma weight residual -60.00 -113.41 53.41 3 1.50e+01 4.44e-03 9.20e+00 ... (remaining 2788 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 426 0.032 - 0.064: 202 0.064 - 0.096: 58 0.096 - 0.128: 60 0.128 - 0.159: 6 Chirality restraints: 752 Sorted by residual: chirality pdb=" CA MET B 958 " pdb=" N MET B 958 " pdb=" C MET B 958 " pdb=" CB MET B 958 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.35e-01 chirality pdb=" CA VAL B 905 " pdb=" N VAL B 905 " pdb=" C VAL B 905 " pdb=" CB VAL B 905 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.10e-01 chirality pdb=" CG LEU B1316 " pdb=" CB LEU B1316 " pdb=" CD1 LEU B1316 " pdb=" CD2 LEU B1316 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.54e-01 ... (remaining 749 not shown) Planarity restraints: 773 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B1317 " 0.036 5.00e-02 4.00e+02 5.50e-02 4.84e+00 pdb=" N PRO B1318 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO B1318 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B1318 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 887 " -0.029 5.00e-02 4.00e+02 4.45e-02 3.16e+00 pdb=" N PRO B 888 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 888 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 888 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU B1512 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.69e+00 pdb=" CD GLU B1512 " -0.028 2.00e-02 2.50e+03 pdb=" OE1 GLU B1512 " 0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU B1512 " 0.010 2.00e-02 2.50e+03 ... (remaining 770 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 4 2.45 - 3.07: 2946 3.07 - 3.68: 6477 3.68 - 4.29: 9700 4.29 - 4.90: 16587 Nonbonded interactions: 35714 Sorted by model distance: nonbonded pdb=" O GLU B 959 " pdb=" OD1 ASP B 960 " model vdw 1.843 3.040 nonbonded pdb=" O GLU B 959 " pdb=" CG ASP B 960 " model vdw 2.381 3.270 nonbonded pdb=" O ASP B1277 " pdb=" OD1 ASP B1277 " model vdw 2.389 3.040 nonbonded pdb=" OG1 THR B1051 " pdb=" O MET B1086 " model vdw 2.453 3.040 nonbonded pdb=" O TYR B 922 " pdb=" OD1 ASP B 923 " model vdw 2.492 3.040 ... (remaining 35709 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: 31.830 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: 0.020 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.180 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 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 : 0.004 0.040 4577 Z= 0.214 Angle : 0.649 10.705 6206 Z= 0.361 Chirality : 0.048 0.159 752 Planarity : 0.004 0.055 773 Dihedral : 15.609 72.439 1693 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.78 % Allowed : 18.22 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 are not related in a simple way. whole: -0.91 (0.36), residues: 554 helix: 1.90 (0.54), residues: 84 sheet: -1.07 (0.32), residues: 270 loop : -0.75 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1206 TYR 0.014 0.001 TYR B 980 PHE 0.016 0.001 PHE B1430 TRP 0.007 0.001 TRP B1340 HIS 0.001 0.000 HIS B 997 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.21 ( 4577) covalent geometry : angle 0.64868 / 0.36 ( 6206) hydrogen bonds : bond 0.09276 / 4.96 ( 87) hydrogen bonds : angle 6.50359 / 4.81 ( 258) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: B 882 LYS cc_start: 0.9079 (tttt) cc_final: 0.8279 (mttt) REVERT: B 884 ARG cc_start: 0.8809 (mtt180) cc_final: 0.7812 (ptt-90) REVERT: B 995 ASP cc_start: 0.8559 (t0) cc_final: 0.8312 (t0) REVERT: B 1068 GLN cc_start: 0.8376 (mm-40) cc_final: 0.8123 (mm110) outliers start: 4 outliers final: 4 residues processed: 77 average time/residue: 0.0801 time to fit residues: 7.8035 Evaluate side-chains 56 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1100 ILE Chi-restraints excluded: chain B residue 1158 VAL Chi-restraints excluded: chain B residue 1219 VAL Chi-restraints excluded: chain B residue 1312 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 54 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.2980 chunk 32 optimal weight: 0.4980 chunk 31 optimal weight: 0.4980 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1222 GLN B1336 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.099707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.078088 restraints weight = 7898.677| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.84 r_work: 0.3056 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4577 Z= 0.164 Angle : 0.505 6.743 6206 Z= 0.264 Chirality : 0.047 0.134 752 Planarity : 0.004 0.055 773 Dihedral : 4.472 24.789 600 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.29 % Allowed : 18.80 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 are not related in a simple way. whole: -0.69 (0.36), residues: 554 helix: 2.13 (0.54), residues: 84 sheet: -1.00 (0.31), residues: 273 loop : -0.52 (0.44), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1206 TYR 0.013 0.002 TYR B 980 PHE 0.015 0.001 PHE B1430 TRP 0.006 0.001 TRP B1340 HIS 0.008 0.001 HIS B 896 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 4577) covalent geometry : angle 0.50470 / 0.26 ( 6206) hydrogen bonds : bond 0.03319 / 2.07 ( 87) hydrogen bonds : angle 4.92286 / 3.42 ( 258) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: B 882 LYS cc_start: 0.9062 (tttt) cc_final: 0.8208 (mttt) REVERT: B 884 ARG cc_start: 0.8794 (mtt180) cc_final: 0.7795 (ptt-90) REVERT: B 945 LYS cc_start: 0.8735 (mmtm) cc_final: 0.8487 (ptpp) outliers start: 17 outliers final: 7 residues processed: 71 average time/residue: 0.0668 time to fit residues: 6.3580 Evaluate side-chains 56 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain B residue 922 TYR Chi-restraints excluded: chain B residue 1173 ASP Chi-restraints excluded: chain B residue 1219 VAL Chi-restraints excluded: chain B residue 1233 ASP Chi-restraints excluded: chain B residue 1312 VAL Chi-restraints excluded: chain B residue 1323 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 0.0070 chunk 54 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 9 optimal weight: 0.1980 chunk 50 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 999 HIS B1228 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.098539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.077650 restraints weight = 8052.150| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.83 r_work: 0.3046 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4577 Z= 0.150 Angle : 0.481 6.982 6206 Z= 0.251 Chirality : 0.046 0.132 752 Planarity : 0.004 0.055 773 Dihedral : 4.298 29.523 597 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.49 % Allowed : 19.38 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 are not related in a simple way. whole: -0.72 (0.36), residues: 554 helix: 2.22 (0.55), residues: 84 sheet: -1.03 (0.31), residues: 269 loop : -0.59 (0.43), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B1206 TYR 0.010 0.001 TYR B 980 PHE 0.016 0.001 PHE B1430 TRP 0.005 0.001 TRP B1340 HIS 0.009 0.001 HIS B 896 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 4577) covalent geometry : angle 0.48119 / 0.25 ( 6206) hydrogen bonds : bond 0.03120 / 1.96 ( 87) hydrogen bonds : angle 4.60895 / 3.16 ( 258) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 51 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: B 882 LYS cc_start: 0.9080 (tttt) cc_final: 0.8136 (mttt) REVERT: B 884 ARG cc_start: 0.8806 (mtt180) cc_final: 0.7765 (ptt-90) outliers start: 18 outliers final: 15 residues processed: 67 average time/residue: 0.0670 time to fit residues: 5.9570 Evaluate side-chains 63 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain B residue 922 TYR Chi-restraints excluded: chain B residue 965 GLU Chi-restraints excluded: chain B residue 1082 SER Chi-restraints excluded: chain B residue 1100 ILE Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1158 VAL Chi-restraints excluded: chain B residue 1173 ASP Chi-restraints excluded: chain B residue 1219 VAL Chi-restraints excluded: chain B residue 1233 ASP Chi-restraints excluded: chain B residue 1312 VAL Chi-restraints excluded: chain B residue 1323 LEU Chi-restraints excluded: chain B residue 1418 THR Chi-restraints excluded: chain B residue 1429 GLU Chi-restraints excluded: chain B residue 1522 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 37 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 55 optimal weight: 0.4980 chunk 22 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.097719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.076888 restraints weight = 7938.398| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.79 r_work: 0.3031 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4577 Z= 0.185 Angle : 0.508 7.043 6206 Z= 0.264 Chirality : 0.047 0.137 752 Planarity : 0.004 0.056 773 Dihedral : 4.471 36.360 597 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.26 % Allowed : 19.96 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 are not related in a simple way. whole: -0.65 (0.36), residues: 554 helix: 2.18 (0.55), residues: 84 sheet: -0.98 (0.32), residues: 270 loop : -0.52 (0.43), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1206 TYR 0.012 0.002 TYR B 980 PHE 0.018 0.002 PHE B1430 TRP 0.005 0.001 TRP B1340 HIS 0.006 0.001 HIS B 896 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 ( 4577) covalent geometry : angle 0.50780 / 0.26 ( 6206) hydrogen bonds : bond 0.03165 / 2.01 ( 87) hydrogen bonds : angle 4.51472 / 3.09 ( 258) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 50 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: B 882 LYS cc_start: 0.9078 (tttt) cc_final: 0.8169 (mttt) REVERT: B 884 ARG cc_start: 0.8813 (mtt180) cc_final: 0.7799 (ptt-90) REVERT: B 1433 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8178 (mt-10) outliers start: 22 outliers final: 16 residues processed: 70 average time/residue: 0.0616 time to fit residues: 5.6448 Evaluate side-chains 65 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain B residue 922 TYR Chi-restraints excluded: chain B residue 965 GLU Chi-restraints excluded: chain B residue 1008 ASN Chi-restraints excluded: chain B residue 1082 SER Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1158 VAL Chi-restraints excluded: chain B residue 1173 ASP Chi-restraints excluded: chain B residue 1219 VAL Chi-restraints excluded: chain B residue 1233 ASP Chi-restraints excluded: chain B residue 1312 VAL Chi-restraints excluded: chain B residue 1323 LEU Chi-restraints excluded: chain B residue 1400 THR Chi-restraints excluded: chain B residue 1418 THR Chi-restraints excluded: chain B residue 1429 GLU Chi-restraints excluded: chain B residue 1433 GLU Chi-restraints excluded: chain B residue 1522 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 33 optimal weight: 0.0040 chunk 53 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 49 optimal weight: 0.0970 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.098123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.077626 restraints weight = 7980.726| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.76 r_work: 0.3049 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4577 Z= 0.128 Angle : 0.469 6.781 6206 Z= 0.244 Chirality : 0.046 0.142 752 Planarity : 0.003 0.055 773 Dihedral : 4.346 37.590 597 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.65 % Allowed : 19.57 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 are not related in a simple way. whole: -0.59 (0.37), residues: 554 helix: 2.29 (0.56), residues: 84 sheet: -0.97 (0.32), residues: 268 loop : -0.49 (0.43), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B1087 TYR 0.008 0.001 TYR B1270 PHE 0.016 0.001 PHE B1430 TRP 0.006 0.001 TRP B1340 HIS 0.006 0.001 HIS B 896 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 4577) covalent geometry : angle 0.46912 / 0.24 ( 6206) hydrogen bonds : bond 0.02972 / 1.92 ( 87) hydrogen bonds : angle 4.28119 / 2.90 ( 258) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 51 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: B 882 LYS cc_start: 0.9043 (tttt) cc_final: 0.8109 (mttt) REVERT: B 884 ARG cc_start: 0.8778 (mtt180) cc_final: 0.7758 (ptt-90) REVERT: B 1068 GLN cc_start: 0.8303 (mm110) cc_final: 0.8034 (mm110) REVERT: B 1257 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8289 (mm) outliers start: 24 outliers final: 18 residues processed: 73 average time/residue: 0.0618 time to fit residues: 6.0324 Evaluate side-chains 66 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 47 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain B residue 922 TYR Chi-restraints excluded: chain B residue 965 GLU Chi-restraints excluded: chain B residue 1008 ASN Chi-restraints excluded: chain B residue 1082 SER Chi-restraints excluded: chain B residue 1100 ILE Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1158 VAL Chi-restraints excluded: chain B residue 1173 ASP Chi-restraints excluded: chain B residue 1219 VAL Chi-restraints excluded: chain B residue 1233 ASP Chi-restraints excluded: chain B residue 1257 ILE Chi-restraints excluded: chain B residue 1291 LEU Chi-restraints excluded: chain B residue 1312 VAL Chi-restraints excluded: chain B residue 1323 LEU Chi-restraints excluded: chain B residue 1400 THR Chi-restraints excluded: chain B residue 1418 THR Chi-restraints excluded: chain B residue 1429 GLU Chi-restraints excluded: chain B residue 1522 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 7 optimal weight: 0.7980 chunk 1 optimal weight: 0.0070 chunk 32 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 6 optimal weight: 0.0980 chunk 52 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 15 optimal weight: 0.0770 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 overall best weight: 0.2956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.099061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.078187 restraints weight = 8090.904| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.84 r_work: 0.3058 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4577 Z= 0.107 Angle : 0.468 6.689 6206 Z= 0.239 Chirality : 0.046 0.132 752 Planarity : 0.003 0.056 773 Dihedral : 4.221 37.797 597 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.68 % Allowed : 19.57 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 are not related in a simple way. whole: -0.52 (0.37), residues: 554 helix: 2.39 (0.56), residues: 84 sheet: -0.94 (0.32), residues: 269 loop : -0.43 (0.43), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B1462 TYR 0.012 0.001 TYR B 980 PHE 0.015 0.001 PHE B1430 TRP 0.006 0.001 TRP B1340 HIS 0.006 0.001 HIS B 896 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 ( 4577) covalent geometry : angle 0.46760 / 0.24 ( 6206) hydrogen bonds : bond 0.02852 / 1.84 ( 87) hydrogen bonds : angle 4.08702 / 2.75 ( 258) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 54 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: B 882 LYS cc_start: 0.9044 (tttt) cc_final: 0.8062 (mttt) REVERT: B 884 ARG cc_start: 0.8768 (mtt180) cc_final: 0.7740 (ptt-90) outliers start: 19 outliers final: 14 residues processed: 71 average time/residue: 0.0661 time to fit residues: 6.3116 Evaluate side-chains 62 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain B residue 922 TYR Chi-restraints excluded: chain B residue 965 GLU Chi-restraints excluded: chain B residue 1082 SER Chi-restraints excluded: chain B residue 1100 ILE Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1158 VAL Chi-restraints excluded: chain B residue 1173 ASP Chi-restraints excluded: chain B residue 1219 VAL Chi-restraints excluded: chain B residue 1233 ASP Chi-restraints excluded: chain B residue 1312 VAL Chi-restraints excluded: chain B residue 1323 LEU Chi-restraints excluded: chain B residue 1400 THR Chi-restraints excluded: chain B residue 1522 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 37 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 0.0060 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.097982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.077260 restraints weight = 8009.193| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.79 r_work: 0.3039 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4577 Z= 0.159 Angle : 0.491 6.970 6206 Z= 0.252 Chirality : 0.046 0.132 752 Planarity : 0.004 0.056 773 Dihedral : 4.372 40.221 597 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.68 % Allowed : 20.16 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 are not related in a simple way. whole: -0.49 (0.37), residues: 554 helix: 2.34 (0.55), residues: 84 sheet: -0.90 (0.32), residues: 271 loop : -0.41 (0.44), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B1206 TYR 0.020 0.001 TYR B 980 PHE 0.017 0.001 PHE B1430 TRP 0.005 0.001 TRP B1340 HIS 0.005 0.001 HIS B 896 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 4577) covalent geometry : angle 0.49146 / 0.25 ( 6206) hydrogen bonds : bond 0.02977 / 1.91 ( 87) hydrogen bonds : angle 4.18050 / 2.82 ( 258) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 50 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: B 882 LYS cc_start: 0.9063 (tttt) cc_final: 0.8132 (mttt) REVERT: B 884 ARG cc_start: 0.8804 (mtt180) cc_final: 0.7755 (ptt-90) REVERT: B 925 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8633 (mtmt) REVERT: B 958 MET cc_start: 0.8264 (ptm) cc_final: 0.7667 (ppp) REVERT: B 1068 GLN cc_start: 0.8282 (mm110) cc_final: 0.8065 (mm110) outliers start: 19 outliers final: 17 residues processed: 68 average time/residue: 0.0588 time to fit residues: 5.1702 Evaluate side-chains 68 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain B residue 925 LYS Chi-restraints excluded: chain B residue 965 GLU Chi-restraints excluded: chain B residue 1008 ASN Chi-restraints excluded: chain B residue 1082 SER Chi-restraints excluded: chain B residue 1100 ILE Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1158 VAL Chi-restraints excluded: chain B residue 1173 ASP Chi-restraints excluded: chain B residue 1219 VAL Chi-restraints excluded: chain B residue 1233 ASP Chi-restraints excluded: chain B residue 1291 LEU Chi-restraints excluded: chain B residue 1312 VAL Chi-restraints excluded: chain B residue 1323 LEU Chi-restraints excluded: chain B residue 1400 THR Chi-restraints excluded: chain B residue 1418 THR Chi-restraints excluded: chain B residue 1429 GLU Chi-restraints excluded: chain B residue 1522 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 7 optimal weight: 0.1980 chunk 39 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.096727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.076092 restraints weight = 8006.746| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.76 r_work: 0.3015 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 4577 Z= 0.209 Angle : 0.527 7.222 6206 Z= 0.271 Chirality : 0.047 0.138 752 Planarity : 0.004 0.056 773 Dihedral : 4.683 43.962 597 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.26 % Allowed : 19.38 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 are not related in a simple way. whole: -0.57 (0.37), residues: 554 helix: 2.39 (0.54), residues: 82 sheet: -0.95 (0.33), residues: 271 loop : -0.47 (0.43), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1206 TYR 0.018 0.001 TYR B 980 PHE 0.021 0.002 PHE B1430 TRP 0.004 0.001 TRP B1340 HIS 0.004 0.001 HIS B 896 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.21 ( 4577) covalent geometry : angle 0.52657 / 0.27 ( 6206) hydrogen bonds : bond 0.03199 / 2.04 ( 87) hydrogen bonds : angle 4.38908 / 2.98 ( 258) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 54 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: B 884 ARG cc_start: 0.8775 (mtt180) cc_final: 0.7793 (ptt-90) REVERT: B 925 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8686 (mtmt) REVERT: B 1323 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9139 (mt) outliers start: 22 outliers final: 15 residues processed: 74 average time/residue: 0.0601 time to fit residues: 5.7636 Evaluate side-chains 66 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 49 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain B residue 925 LYS Chi-restraints excluded: chain B residue 965 GLU Chi-restraints excluded: chain B residue 1008 ASN Chi-restraints excluded: chain B residue 1082 SER Chi-restraints excluded: chain B residue 1100 ILE Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1158 VAL Chi-restraints excluded: chain B residue 1173 ASP Chi-restraints excluded: chain B residue 1219 VAL Chi-restraints excluded: chain B residue 1233 ASP Chi-restraints excluded: chain B residue 1291 LEU Chi-restraints excluded: chain B residue 1312 VAL Chi-restraints excluded: chain B residue 1323 LEU Chi-restraints excluded: chain B residue 1400 THR Chi-restraints excluded: chain B residue 1429 GLU Chi-restraints excluded: chain B residue 1522 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 15 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 33 optimal weight: 0.0010 chunk 32 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 45 optimal weight: 0.0010 chunk 12 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1099 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.098176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.077424 restraints weight = 7964.128| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.77 r_work: 0.3047 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4577 Z= 0.131 Angle : 0.503 6.932 6206 Z= 0.258 Chirality : 0.046 0.129 752 Planarity : 0.003 0.056 773 Dihedral : 4.503 43.710 597 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.68 % Allowed : 20.35 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 are not related in a simple way. whole: -0.57 (0.37), residues: 554 helix: 2.54 (0.56), residues: 82 sheet: -0.94 (0.33), residues: 269 loop : -0.57 (0.43), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B1462 TYR 0.013 0.001 TYR B 980 PHE 0.017 0.001 PHE B1430 TRP 0.007 0.001 TRP B1340 HIS 0.005 0.001 HIS B 896 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 4577) covalent geometry : angle 0.50293 / 0.26 ( 6206) hydrogen bonds : bond 0.02960 / 1.91 ( 87) hydrogen bonds : angle 4.19262 / 2.83 ( 258) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 52 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 884 ARG cc_start: 0.8776 (mtt180) cc_final: 0.7745 (ptt-90) REVERT: B 925 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8644 (mtmt) REVERT: B 958 MET cc_start: 0.8262 (ptm) cc_final: 0.7642 (ppp) outliers start: 19 outliers final: 17 residues processed: 69 average time/residue: 0.0640 time to fit residues: 5.8634 Evaluate side-chains 68 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain B residue 925 LYS Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 965 GLU Chi-restraints excluded: chain B residue 1008 ASN Chi-restraints excluded: chain B residue 1082 SER Chi-restraints excluded: chain B residue 1100 ILE Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1158 VAL Chi-restraints excluded: chain B residue 1173 ASP Chi-restraints excluded: chain B residue 1219 VAL Chi-restraints excluded: chain B residue 1233 ASP Chi-restraints excluded: chain B residue 1291 LEU Chi-restraints excluded: chain B residue 1312 VAL Chi-restraints excluded: chain B residue 1323 LEU Chi-restraints excluded: chain B residue 1400 THR Chi-restraints excluded: chain B residue 1429 GLU Chi-restraints excluded: chain B residue 1522 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 50 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 1 optimal weight: 0.0980 chunk 19 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 23 optimal weight: 0.1980 chunk 33 optimal weight: 0.6980 chunk 3 optimal weight: 0.3980 chunk 24 optimal weight: 0.0970 overall best weight: 0.2778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.098945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.078287 restraints weight = 7992.867| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.78 r_work: 0.3064 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4577 Z= 0.109 Angle : 0.482 7.030 6206 Z= 0.246 Chirality : 0.046 0.128 752 Planarity : 0.003 0.055 773 Dihedral : 4.335 43.410 597 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.29 % Allowed : 21.32 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 are not related in a simple way. whole: -0.48 (0.37), residues: 554 helix: 2.56 (0.56), residues: 83 sheet: -0.83 (0.33), residues: 271 loop : -0.60 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B1087 TYR 0.013 0.001 TYR B 895 PHE 0.015 0.001 PHE B1430 TRP 0.012 0.001 TRP B1340 HIS 0.005 0.001 HIS B 896 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 4577) covalent geometry : angle 0.48150 / 0.25 ( 6206) hydrogen bonds : bond 0.02788 / 1.81 ( 87) hydrogen bonds : angle 3.97950 / 2.66 ( 258) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: B 884 ARG cc_start: 0.8772 (mtt180) cc_final: 0.7709 (ptt-90) REVERT: B 925 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8632 (mtmt) REVERT: B 958 MET cc_start: 0.8284 (ptm) cc_final: 0.7742 (ppp) REVERT: B 1068 GLN cc_start: 0.8287 (mm110) cc_final: 0.7034 (mm-40) outliers start: 17 outliers final: 16 residues processed: 69 average time/residue: 0.0570 time to fit residues: 5.3719 Evaluate side-chains 66 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 49 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain B residue 925 LYS Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 965 GLU Chi-restraints excluded: chain B residue 1008 ASN Chi-restraints excluded: chain B residue 1082 SER Chi-restraints excluded: chain B residue 1100 ILE Chi-restraints excluded: chain B residue 1158 VAL Chi-restraints excluded: chain B residue 1173 ASP Chi-restraints excluded: chain B residue 1219 VAL Chi-restraints excluded: chain B residue 1233 ASP Chi-restraints excluded: chain B residue 1291 LEU Chi-restraints excluded: chain B residue 1312 VAL Chi-restraints excluded: chain B residue 1323 LEU Chi-restraints excluded: chain B residue 1400 THR Chi-restraints excluded: chain B residue 1429 GLU Chi-restraints excluded: chain B residue 1522 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 chunk 24 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.096904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.076127 restraints weight = 8113.273| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.78 r_work: 0.3019 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 4577 Z= 0.211 Angle : 0.543 7.373 6206 Z= 0.281 Chirality : 0.047 0.137 752 Planarity : 0.004 0.055 773 Dihedral : 4.628 46.079 597 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.49 % Allowed : 21.12 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 are not related in a simple way. whole: -0.55 (0.37), residues: 554 helix: 2.45 (0.56), residues: 82 sheet: -0.89 (0.33), residues: 271 loop : -0.56 (0.44), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1206 TYR 0.018 0.002 TYR B 980 PHE 0.019 0.002 PHE B1430 TRP 0.008 0.001 TRP B1340 HIS 0.004 0.001 HIS B 896 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.21 ( 4577) covalent geometry : angle 0.54302 / 0.28 ( 6206) hydrogen bonds : bond 0.03193 / 2.01 ( 87) hydrogen bonds : angle 4.22094 / 2.86 ( 258) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1783.06 seconds wall clock time: 31 minutes 20.64 seconds (1880.64 seconds total)