Starting phenix.real_space_refine on Wed Aug 5 05:43:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wad_65812/08_2026/9wad_65812.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wad_65812/08_2026/9wad_65812.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wad_65812/08_2026/9wad_65812.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wad_65812/08_2026/9wad_65812.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wad_65812/08_2026/9wad_65812.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wad_65812/08_2026/9wad_65812.map" } resolution = 3.15 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= 0.040 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: 5 Type Number sf(0) Gaussians P 141 5.49 5 S 18 5.16 5 C 4911 2.51 5 N 1565 2.21 5 O 1955 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8590 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5625 Classifications: {'peptide': 701} Link IDs: {'PTRANS': 26, 'TRANS': 674} Chain breaks: 10 Chain: "B" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 2035 Classifications: {'RNA': 96} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 5, 'rna3p_pur': 45, 'rna3p_pyr': 44} Link IDs: {'rna2p': 6, 'rna3p': 89} Chain breaks: 3 Chain: "C" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 705 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "D" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 225 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Time building chain proxies: 1.92, per 1000 atoms: 0.22 Number of scatterers: 8590 At special positions: 0 Unit cell: (85.075, 103.525, 125.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 P 141 15.00 O 1955 8.00 N 1565 7.00 C 4911 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: 0.78 Conformation dependent library (CDL) restraints added in 149.7 milliseconds 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1306 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 7 sheets defined 42.1% alpha, 11.4% beta 57 base pairs and 89 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 54 through 84 Processing helix chain 'A' and resid 91 through 96 removed outlier: 3.799A pdb=" N TYR A 96 " --> pdb=" O ILE A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 118 through 132 Processing helix chain 'A' and resid 149 through 166 Processing helix chain 'A' and resid 169 through 178 removed outlier: 3.679A pdb=" N MET A 173 " --> pdb=" O THR A 169 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A 174 " --> pdb=" O VAL A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 230 Processing helix chain 'A' and resid 235 through 247 Processing helix chain 'A' and resid 297 through 311 Processing helix chain 'A' and resid 329 through 341 removed outlier: 3.677A pdb=" N TYR A 341 " --> pdb=" O ILE A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 399 removed outlier: 3.512A pdb=" N HIS A 389 " --> pdb=" O MET A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 420 Processing helix chain 'A' and resid 422 through 433 removed outlier: 3.870A pdb=" N THR A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU A 433 " --> pdb=" O LYS A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 444 Processing helix chain 'A' and resid 456 through 469 Proline residue: A 464 - end of helix Processing helix chain 'A' and resid 471 through 480 Processing helix chain 'A' and resid 505 through 526 removed outlier: 4.050A pdb=" N ALA A 511 " --> pdb=" O VAL A 507 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL A 518 " --> pdb=" O GLN A 514 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N HIS A 526 " --> pdb=" O VAL A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 706 Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 914 through 916 No H-bonds generated for 'chain 'A' and resid 914 through 916' Processing helix chain 'A' and resid 933 through 947 removed outlier: 3.504A pdb=" N PHE A 947 " --> pdb=" O ARG A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 955 removed outlier: 3.528A pdb=" N PHE A 955 " --> pdb=" O ALA A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1023 removed outlier: 3.595A pdb=" N LEU A1022 " --> pdb=" O ALA A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1040 Processing sheet with id=AA1, first strand: chain 'A' and resid 292 through 294 removed outlier: 5.509A pdb=" N LEU A 454 " --> pdb=" O ALA A 293 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 346 through 347 removed outlier: 6.893A pdb=" N ILE A 346 " --> pdb=" O PHE A 382 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 890 through 894 Processing sheet with id=AA4, first strand: chain 'A' and resid 959 through 962 removed outlier: 3.918A pdb=" N VAL A 959 " --> pdb=" O VAL A 972 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR A 970 " --> pdb=" O LYS A 961 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 984 through 987 Processing sheet with id=AA6, first strand: chain 'A' and resid 1015 through 1017 removed outlier: 3.562A pdb=" N ARG A1001 " --> pdb=" O ILE A1016 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL A1004 " --> pdb=" O PHE A1051 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N PHE A1051 " --> pdb=" O VAL A1004 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ALA A1006 " --> pdb=" O PHE A1049 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N PHE A1049 " --> pdb=" O ALA A1006 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1105 through 1109 removed outlier: 3.704A pdb=" N LEU A1097 " --> pdb=" O LEU A1106 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLY A1108 " --> pdb=" O LEU A1095 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU A1095 " --> pdb=" O GLY A1108 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY A1087 " --> pdb=" O THR A1096 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ARG A1098 " --> pdb=" O PHE A1085 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N PHE A1085 " --> pdb=" O ARG A1098 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA A1058 " --> pdb=" O TYR A1120 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL A1116 " --> pdb=" O LYS A1062 " (cutoff:3.500A) 221 hydrogen bonds defined for protein. 636 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 143 hydrogen bonds 278 hydrogen bond angles 0 basepair planarities 57 basepair parallelities 89 stacking parallelities Total time for adding SS restraints: 1.69 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1209 1.32 - 1.44: 3098 1.44 - 1.57: 4417 1.57 - 1.69: 276 1.69 - 1.81: 30 Bond restraints: 9030 Sorted by residual: bond pdb=" C3' DC D 4 " pdb=" C2' DC D 4 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DC C 14 " pdb=" C2' DC C 14 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.43e+00 bond pdb=" N VAL A1042 " pdb=" CA VAL A1042 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.21e-02 6.83e+03 8.17e+00 bond pdb=" C PRO A 971 " pdb=" O PRO A 971 " ideal model delta sigma weight residual 1.233 1.201 0.032 1.12e-02 7.97e+03 8.14e+00 bond pdb=" N ARG A 877 " pdb=" CA ARG A 877 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.06e-02 8.90e+03 8.01e+00 ... (remaining 9025 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 12046 1.47 - 2.94: 708 2.94 - 4.40: 50 4.40 - 5.87: 9 5.87 - 7.34: 3 Bond angle restraints: 12816 Sorted by residual: angle pdb=" C1' C B 12 " pdb=" N1 C B 12 " pdb=" C2 C B 12 " ideal model delta sigma weight residual 118.80 124.55 -5.75 1.10e+00 8.26e-01 2.73e+01 angle pdb=" O5' A B 54 " pdb=" C5' A B 54 " pdb=" C4' A B 54 " ideal model delta sigma weight residual 109.40 113.55 -4.15 8.00e-01 1.56e+00 2.69e+01 angle pdb=" N3 DT C 6 " pdb=" C4 DT C 6 " pdb=" O4 DT C 6 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT C -1 " pdb=" C4 DT C -1 " pdb=" O4 DT C -1 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT C 1 " pdb=" C4 DT C 1 " pdb=" O4 DT C 1 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.77e+01 ... (remaining 12811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.79: 4868 29.79 - 59.59: 497 59.59 - 89.38: 85 89.38 - 119.17: 0 119.17 - 148.97: 1 Dihedral angle restraints: 5451 sinusoidal: 3426 harmonic: 2025 Sorted by residual: dihedral pdb=" C4' G B 45 " pdb=" C3' G B 45 " pdb=" O3' G B 45 " pdb=" P A B 46 " ideal model delta sinusoidal sigma weight residual 220.00 71.03 148.97 1 3.50e+01 8.16e-04 1.46e+01 dihedral pdb=" CA VAL A 199 " pdb=" C VAL A 199 " pdb=" N ARG A 200 " pdb=" CA ARG A 200 " ideal model delta harmonic sigma weight residual 180.00 163.87 16.13 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" O4' A B 39 " pdb=" C1' A B 39 " pdb=" N9 A B 39 " pdb=" C4 A B 39 " ideal model delta sinusoidal sigma weight residual -106.00 -152.31 46.31 1 1.70e+01 3.46e-03 1.03e+01 ... (remaining 5448 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1153 0.049 - 0.098: 221 0.098 - 0.148: 132 0.148 - 0.197: 5 0.197 - 0.246: 1 Chirality restraints: 1512 Sorted by residual: chirality pdb=" CA VAL A 972 " pdb=" N VAL A 972 " pdb=" C VAL A 972 " pdb=" CB VAL A 972 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CB VAL A 972 " pdb=" CA VAL A 972 " pdb=" CG1 VAL A 972 " pdb=" CG2 VAL A 972 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.94e-01 chirality pdb=" CA ILE A 704 " pdb=" N ILE A 704 " pdb=" C ILE A 704 " pdb=" CB ILE A 704 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.21e-01 ... (remaining 1509 not shown) Planarity restraints: 1123 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 268 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO A 269 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 269 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 269 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 82 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.88e+00 pdb=" CD GLU A 82 " -0.024 2.00e-02 2.50e+03 pdb=" OE1 GLU A 82 " 0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU A 82 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A1014 " -0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO A1015 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A1015 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A1015 " -0.018 5.00e-02 4.00e+02 ... (remaining 1120 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 688 2.73 - 3.27: 7928 3.27 - 3.82: 15253 3.82 - 4.36: 18863 4.36 - 4.90: 29162 Nonbonded interactions: 71894 Sorted by model distance: nonbonded pdb=" OG SER A 197 " pdb=" OD1 ASN A 198 " model vdw 2.191 3.040 nonbonded pdb=" O LEU A 126 " pdb=" OH TYR A 242 " model vdw 2.210 3.040 nonbonded pdb=" OG SER A1091 " pdb=" OP2 DC D 5 " model vdw 2.225 3.040 nonbonded pdb=" NH1 ARG A 69 " pdb=" OP1 A B 20 " model vdw 2.234 3.120 nonbonded pdb=" O2 C B 89 " pdb=" N4 C B 91 " model vdw 2.266 3.120 ... (remaining 71889 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 8.830 Find NCS groups from input model: 0.040 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 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 0.036 9030 Z= 0.314 Angle : 0.699 7.341 12816 Z= 0.556 Chirality : 0.051 0.246 1512 Planarity : 0.003 0.042 1123 Dihedral : 20.775 148.968 4145 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 0.00 % Allowed : 18.68 % Favored : 81.32 % 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 are not related in a simple way. whole: -0.04 (0.32), residues: 679 helix: 1.61 (0.32), residues: 276 sheet: -2.12 (0.71), residues: 53 loop : -1.04 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 352 TYR 0.014 0.001 TYR A 96 PHE 0.014 0.001 PHE A 300 TRP 0.005 0.001 TRP A 75 HIS 0.004 0.001 HIS A 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.31 ( 9030) covalent geometry : angle 0.69872 / 0.56 (12816) hydrogen bonds : bond 0.11849 / 8.50 ( 364) hydrogen bonds : angle 4.70950 / 3.26 ( 914) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.251 Fit side-chains REVERT: A 1022 LEU cc_start: 0.7962 (mt) cc_final: 0.7601 (mt) REVERT: A 1060 MET cc_start: 0.6811 (mmp) cc_final: 0.6570 (mmp) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.0990 time to fit residues: 9.9306 Evaluate side-chains 67 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 0.0870 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN A 996 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.214048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.184699 restraints weight = 9907.081| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 1.22 r_work: 0.3958 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3838 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.0655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9030 Z= 0.130 Angle : 0.498 5.581 12816 Z= 0.292 Chirality : 0.035 0.218 1512 Planarity : 0.004 0.042 1123 Dihedral : 21.155 148.937 2732 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.98 % Allowed : 17.69 % Favored : 80.33 % 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 are not related in a simple way. whole: 0.09 (0.32), residues: 679 helix: 1.76 (0.32), residues: 272 sheet: -2.10 (0.71), residues: 49 loop : -0.99 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 352 TYR 0.019 0.001 TYR A 96 PHE 0.014 0.001 PHE A 300 TRP 0.005 0.001 TRP A 75 HIS 0.003 0.001 HIS A 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.13 ( 9030) covalent geometry : angle 0.49802 / 0.29 (12816) hydrogen bonds : bond 0.05067 / 3.42 ( 364) hydrogen bonds : angle 3.90228 / 2.71 ( 914) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.246 Fit side-chains REVERT: A 200 ARG cc_start: 0.7404 (mtt180) cc_final: 0.7179 (mtt180) REVERT: A 704 ILE cc_start: 0.3660 (OUTLIER) cc_final: 0.3307 (mt) REVERT: A 1022 LEU cc_start: 0.7852 (mt) cc_final: 0.7446 (mt) outliers start: 12 outliers final: 8 residues processed: 86 average time/residue: 0.1155 time to fit residues: 12.8272 Evaluate side-chains 79 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 920 LYS Chi-restraints excluded: chain A residue 973 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 HIS ** A 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.208167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.178437 restraints weight = 9787.328| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 1.25 r_work: 0.3902 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3777 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9030 Z= 0.167 Angle : 0.538 8.550 12816 Z= 0.303 Chirality : 0.037 0.215 1512 Planarity : 0.005 0.056 1123 Dihedral : 21.063 149.587 2732 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.97 % Allowed : 17.36 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.10 (0.32), residues: 679 helix: 1.55 (0.31), residues: 272 sheet: -2.11 (0.70), residues: 49 loop : -1.07 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 969 TYR 0.016 0.001 TYR A 96 PHE 0.014 0.002 PHE A 300 TRP 0.007 0.001 TRP A 715 HIS 0.004 0.001 HIS A 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.17 ( 9030) covalent geometry : angle 0.53847 / 0.30 (12816) hydrogen bonds : bond 0.05109 / 3.44 ( 364) hydrogen bonds : angle 3.75483 / 2.63 ( 914) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 75 time to evaluate : 0.157 Fit side-chains REVERT: A 200 ARG cc_start: 0.7444 (mtt180) cc_final: 0.7206 (mtt180) outliers start: 24 outliers final: 16 residues processed: 91 average time/residue: 0.0801 time to fit residues: 10.1536 Evaluate side-chains 85 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 920 LYS Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1111 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 43 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 193 HIS A 425 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.209997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.179876 restraints weight = 9925.591| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 1.29 r_work: 0.3937 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3814 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9030 Z= 0.127 Angle : 0.494 10.179 12816 Z= 0.283 Chirality : 0.035 0.214 1512 Planarity : 0.004 0.049 1123 Dihedral : 21.023 149.977 2732 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.14 % Allowed : 17.85 % Favored : 79.01 % 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 are not related in a simple way. whole: 0.04 (0.32), residues: 679 helix: 1.71 (0.31), residues: 272 sheet: -1.98 (0.72), residues: 49 loop : -1.03 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 969 TYR 0.015 0.001 TYR A 96 PHE 0.014 0.001 PHE A 300 TRP 0.005 0.001 TRP A 715 HIS 0.003 0.001 HIS A 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.13 ( 9030) covalent geometry : angle 0.49384 / 0.28 (12816) hydrogen bonds : bond 0.04656 / 3.14 ( 364) hydrogen bonds : angle 3.62908 / 2.54 ( 914) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.186 Fit side-chains REVERT: A 353 LYS cc_start: 0.7257 (pptt) cc_final: 0.6323 (tptt) REVERT: A 1041 ARG cc_start: 0.8052 (mtm-85) cc_final: 0.7495 (mtm-85) outliers start: 19 outliers final: 14 residues processed: 87 average time/residue: 0.0874 time to fit residues: 10.3257 Evaluate side-chains 84 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 973 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 53 optimal weight: 0.9990 chunk 45 optimal weight: 0.0570 chunk 5 optimal weight: 0.0670 chunk 12 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 72 optimal weight: 8.9990 chunk 30 optimal weight: 0.9980 chunk 21 optimal weight: 0.0970 chunk 60 optimal weight: 2.9990 overall best weight: 0.4434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 264 HIS A 396 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.215377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.186463 restraints weight = 10008.821| |-----------------------------------------------------------------------------| r_work (start): 0.4093 rms_B_bonded: 1.15 r_work: 0.3962 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3838 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9030 Z= 0.109 Angle : 0.465 8.276 12816 Z= 0.269 Chirality : 0.034 0.212 1512 Planarity : 0.004 0.051 1123 Dihedral : 20.960 150.212 2732 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.14 % Allowed : 18.35 % Favored : 78.51 % 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 are not related in a simple way. whole: 0.31 (0.33), residues: 679 helix: 1.89 (0.32), residues: 277 sheet: -1.83 (0.72), residues: 49 loop : -0.89 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 969 TYR 0.013 0.001 TYR A 96 PHE 0.012 0.001 PHE A 300 TRP 0.004 0.001 TRP A 75 HIS 0.003 0.001 HIS A 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.11 ( 9030) covalent geometry : angle 0.46496 / 0.27 (12816) hydrogen bonds : bond 0.04291 / 2.89 ( 364) hydrogen bonds : angle 3.48492 / 2.44 ( 914) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.223 Fit side-chains REVERT: A 353 LYS cc_start: 0.7226 (pptt) cc_final: 0.6350 (tptt) REVERT: A 1041 ARG cc_start: 0.7917 (mtm-85) cc_final: 0.7432 (mtm-85) outliers start: 19 outliers final: 13 residues processed: 92 average time/residue: 0.0847 time to fit residues: 10.4880 Evaluate side-chains 83 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1004 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 63 optimal weight: 6.9990 chunk 27 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 396 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.208628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.178906 restraints weight = 9893.542| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 1.26 r_work: 0.3918 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3795 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9030 Z= 0.155 Angle : 0.519 8.434 12816 Z= 0.291 Chirality : 0.036 0.211 1512 Planarity : 0.004 0.040 1123 Dihedral : 20.958 150.197 2732 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.31 % Allowed : 18.68 % Favored : 78.02 % 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 are not related in a simple way. whole: 0.06 (0.32), residues: 679 helix: 1.63 (0.31), residues: 274 sheet: -1.90 (0.71), residues: 49 loop : -0.95 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 279 TYR 0.021 0.001 TYR A 96 PHE 0.014 0.002 PHE A1117 TRP 0.011 0.002 TRP A 420 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.16 ( 9030) covalent geometry : angle 0.51935 / 0.29 (12816) hydrogen bonds : bond 0.04728 / 3.16 ( 364) hydrogen bonds : angle 3.57099 / 2.52 ( 914) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.270 Fit side-chains REVERT: A 200 ARG cc_start: 0.7473 (ttt-90) cc_final: 0.6815 (ttp-170) REVERT: A 353 LYS cc_start: 0.7263 (pptt) cc_final: 0.6325 (tptt) REVERT: A 1060 MET cc_start: 0.6508 (mmp) cc_final: 0.6092 (mmp) outliers start: 20 outliers final: 18 residues processed: 88 average time/residue: 0.0838 time to fit residues: 10.2719 Evaluate side-chains 86 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1004 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 9.9990 chunk 67 optimal weight: 0.0000 chunk 60 optimal weight: 0.9980 chunk 28 optimal weight: 0.0770 chunk 27 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 51 optimal weight: 0.3980 chunk 63 optimal weight: 0.1980 overall best weight: 0.3342 ------------------------------------------------------------------------------- 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 = 0.4370 r_free = 0.4370 target = 0.214942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.185922 restraints weight = 10103.416| |-----------------------------------------------------------------------------| r_work (start): 0.4090 rms_B_bonded: 1.20 r_work: 0.3954 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3833 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9030 Z= 0.105 Angle : 0.460 6.749 12816 Z= 0.267 Chirality : 0.033 0.212 1512 Planarity : 0.004 0.039 1123 Dihedral : 20.936 150.171 2732 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.31 % Allowed : 20.00 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.33 (0.33), residues: 679 helix: 1.88 (0.31), residues: 279 sheet: -1.80 (0.73), residues: 49 loop : -0.85 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1041 TYR 0.017 0.001 TYR A 96 PHE 0.014 0.001 PHE A 300 TRP 0.006 0.001 TRP A1040 HIS 0.002 0.000 HIS A 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.11 ( 9030) covalent geometry : angle 0.45971 / 0.27 (12816) hydrogen bonds : bond 0.04207 / 2.82 ( 364) hydrogen bonds : angle 3.44760 / 2.42 ( 914) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.237 Fit side-chains REVERT: A 200 ARG cc_start: 0.7438 (ttt-90) cc_final: 0.6907 (ttp-170) REVERT: A 353 LYS cc_start: 0.7242 (pptt) cc_final: 0.6393 (tptt) outliers start: 14 outliers final: 13 residues processed: 82 average time/residue: 0.0855 time to fit residues: 9.8448 Evaluate side-chains 80 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 968 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 0.0770 chunk 16 optimal weight: 0.9980 chunk 73 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 69 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 31 optimal weight: 10.0000 overall best weight: 1.1740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 396 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.211617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.182378 restraints weight = 9982.003| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 1.18 r_work: 0.3917 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3798 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9030 Z= 0.148 Angle : 0.516 7.106 12816 Z= 0.289 Chirality : 0.036 0.212 1512 Planarity : 0.004 0.039 1123 Dihedral : 20.893 150.070 2732 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.14 % Allowed : 19.83 % Favored : 77.02 % 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 are not related in a simple way. whole: 0.14 (0.32), residues: 679 helix: 1.68 (0.31), residues: 274 sheet: -1.83 (0.70), residues: 49 loop : -0.89 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1041 TYR 0.016 0.001 TYR A 96 PHE 0.013 0.002 PHE A 300 TRP 0.007 0.001 TRP A 715 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 ( 9030) covalent geometry : angle 0.51616 / 0.29 (12816) hydrogen bonds : bond 0.04671 / 3.11 ( 364) hydrogen bonds : angle 3.53295 / 2.50 ( 914) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.185 Fit side-chains REVERT: A 353 LYS cc_start: 0.7264 (pptt) cc_final: 0.6366 (tptt) REVERT: A 1060 MET cc_start: 0.6696 (mmp) cc_final: 0.6165 (mmp) outliers start: 19 outliers final: 18 residues processed: 88 average time/residue: 0.0847 time to fit residues: 10.5001 Evaluate side-chains 88 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1004 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 6 optimal weight: 3.9990 chunk 13 optimal weight: 0.0020 chunk 21 optimal weight: 0.0570 chunk 36 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.8112 ------------------------------------------------------------------------------- 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 = 0.4353 r_free = 0.4353 target = 0.212859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.183913 restraints weight = 9978.412| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 1.17 r_work: 0.3938 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3816 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9030 Z= 0.123 Angle : 0.482 5.739 12816 Z= 0.276 Chirality : 0.034 0.214 1512 Planarity : 0.004 0.039 1123 Dihedral : 20.870 149.975 2732 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.64 % Allowed : 19.50 % Favored : 76.86 % 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 are not related in a simple way. whole: 0.27 (0.32), residues: 679 helix: 1.73 (0.31), residues: 277 sheet: -1.75 (0.72), residues: 49 loop : -0.79 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1041 TYR 0.016 0.001 TYR A 96 PHE 0.013 0.001 PHE A 300 TRP 0.005 0.001 TRP A 75 HIS 0.002 0.001 HIS A 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 ( 9030) covalent geometry : angle 0.48224 / 0.28 (12816) hydrogen bonds : bond 0.04388 / 2.93 ( 364) hydrogen bonds : angle 3.48601 / 2.46 ( 914) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.250 Fit side-chains REVERT: A 200 ARG cc_start: 0.7856 (ttt-90) cc_final: 0.7177 (ttp-170) REVERT: A 353 LYS cc_start: 0.7252 (pptt) cc_final: 0.6363 (tptt) REVERT: A 1060 MET cc_start: 0.6686 (mmp) cc_final: 0.6123 (mmt) outliers start: 22 outliers final: 20 residues processed: 87 average time/residue: 0.1102 time to fit residues: 12.8742 Evaluate side-chains 89 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 973 ARG Chi-restraints excluded: chain A residue 1004 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 48 optimal weight: 0.3980 chunk 64 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 77 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 21 optimal weight: 0.1980 chunk 66 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 396 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.210126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.181189 restraints weight = 9954.363| |-----------------------------------------------------------------------------| r_work (start): 0.4043 rms_B_bonded: 1.15 r_work: 0.3909 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3787 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 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 : 0.004 0.041 9030 Z= 0.172 Angle : 0.537 6.299 12816 Z= 0.298 Chirality : 0.037 0.214 1512 Planarity : 0.004 0.039 1123 Dihedral : 20.885 150.021 2732 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.14 % Allowed : 20.17 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.05 (0.32), residues: 679 helix: 1.48 (0.31), residues: 277 sheet: -1.82 (0.71), residues: 49 loop : -0.86 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 352 TYR 0.016 0.001 TYR A 96 PHE 0.013 0.002 PHE A1117 TRP 0.007 0.002 TRP A 715 HIS 0.004 0.001 HIS A 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 ( 9030) covalent geometry : angle 0.53661 / 0.30 (12816) hydrogen bonds : bond 0.04842 / 3.22 ( 364) hydrogen bonds : angle 3.58462 / 2.54 ( 914) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1358 Ramachandran restraints generated. 679 Oldfield, 0 Emsley, 679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.193 Fit side-chains REVERT: A 200 ARG cc_start: 0.7818 (ttt-90) cc_final: 0.7081 (ttp-170) REVERT: A 353 LYS cc_start: 0.7293 (pptt) cc_final: 0.6250 (tptt) REVERT: A 1060 MET cc_start: 0.6748 (mmp) cc_final: 0.6263 (mmt) outliers start: 19 outliers final: 19 residues processed: 88 average time/residue: 0.0871 time to fit residues: 10.8250 Evaluate side-chains 91 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1004 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 65 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 12 optimal weight: 0.0770 chunk 16 optimal weight: 0.7980 chunk 79 optimal weight: 10.0000 chunk 22 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- 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 = 0.4332 r_free = 0.4332 target = 0.209675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.181355 restraints weight = 9814.023| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 1.15 r_work: 0.3933 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3810 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9030 Z= 0.120 Angle : 0.486 6.015 12816 Z= 0.278 Chirality : 0.034 0.215 1512 Planarity : 0.004 0.039 1123 Dihedral : 20.867 149.947 2732 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.31 % Allowed : 19.34 % Favored : 77.36 % 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 are not related in a simple way. whole: 0.27 (0.32), residues: 679 helix: 1.74 (0.31), residues: 276 sheet: -1.74 (0.72), residues: 49 loop : -0.81 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1041 TYR 0.030 0.001 TYR A 242 PHE 0.013 0.001 PHE A 300 TRP 0.005 0.001 TRP A 75 HIS 0.002 0.001 HIS A 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 ( 9030) covalent geometry : angle 0.48550 / 0.28 (12816) hydrogen bonds : bond 0.04463 / 2.96 ( 364) hydrogen bonds : angle 3.48391 / 2.46 ( 914) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2028.04 seconds wall clock time: 35 minutes 20.67 seconds (2120.67 seconds total)