Starting phenix.real_space_refine on Sat Aug 23 03:36:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bit_44601/08_2025/9bit_44601_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bit_44601/08_2025/9bit_44601.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bit_44601/08_2025/9bit_44601_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bit_44601/08_2025/9bit_44601_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bit_44601/08_2025/9bit_44601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bit_44601/08_2025/9bit_44601.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 34 5.16 5 Cl 1 4.86 5 C 3101 2.51 5 N 767 2.21 5 O 811 1.98 5 H 4734 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9448 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 7529 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 21, 'TRANS': 450} Chain breaks: 1 Chain: "B" Number of atoms: 1890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1890 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'CXN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.67, per 1000 atoms: 0.18 Number of scatterers: 9448 At special positions: 0 Unit cell: (87.108, 109.8, 83.448, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 34 16.00 O 811 8.00 N 767 7.00 C 3101 6.00 H 4734 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 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: 0.72 Conformation dependent library (CDL) restraints added in 333.5 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1104 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 2 sheets defined 64.0% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 43 through 45 No H-bonds generated for 'chain 'A' and resid 43 through 45' Processing helix chain 'A' and resid 46 through 74 removed outlier: 5.106A pdb=" N ASN A 52 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL A 66 " --> pdb=" O GLY A 62 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N LEU A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 96 Processing helix chain 'A' and resid 96 through 107 Processing helix chain 'A' and resid 112 through 132 removed outlier: 3.534A pdb=" N ALA A 132 " --> pdb=" O LYS A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 171 removed outlier: 4.234A pdb=" N GLY A 159 " --> pdb=" O LEU A 155 " (cutoff:3.500A) Proline residue: A 162 - end of helix removed outlier: 3.790A pdb=" N ALA A 165 " --> pdb=" O LYS A 161 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN A 171 " --> pdb=" O PHE A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 206 removed outlier: 3.573A pdb=" N ARG A 180 " --> pdb=" O HIS A 176 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR A 181 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG A 182 " --> pdb=" O GLU A 178 " (cutoff:3.500A) Proline residue: A 203 - end of helix removed outlier: 3.590A pdb=" N ARG A 206 " --> pdb=" O THR A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 238 removed outlier: 3.971A pdb=" N ALA A 220 " --> pdb=" O CYS A 216 " (cutoff:3.500A) Proline residue: A 224 - end of helix removed outlier: 3.710A pdb=" N GLY A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 242 Processing helix chain 'A' and resid 250 through 266 removed outlier: 3.870A pdb=" N ARG A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 307 removed outlier: 3.974A pdb=" N ASP A 295 " --> pdb=" O HIS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 318 removed outlier: 3.674A pdb=" N PHE A 312 " --> pdb=" O PRO A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 329 removed outlier: 3.595A pdb=" N LEU A 325 " --> pdb=" O SER A 321 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 345 Processing helix chain 'A' and resid 346 through 362 removed outlier: 3.576A pdb=" N PHE A 350 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Proline residue: A 357 - end of helix Processing helix chain 'A' and resid 362 through 370 removed outlier: 3.913A pdb=" N CYS A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 403 Processing helix chain 'A' and resid 611 through 636 removed outlier: 3.532A pdb=" N GLU A 631 " --> pdb=" O VAL A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 642 removed outlier: 3.887A pdb=" N LYS A 642 " --> pdb=" O SER A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 665 removed outlier: 3.794A pdb=" N VAL A 653 " --> pdb=" O TRP A 649 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLN A 665 " --> pdb=" O LEU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 695 Processing helix chain 'B' and resid 28 through 30 No H-bonds generated for 'chain 'B' and resid 28 through 30' Processing helix chain 'B' and resid 53 through 56 removed outlier: 4.209A pdb=" N ARG B 56 " --> pdb=" O TRP B 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 53 through 56' Processing helix chain 'B' and resid 110 through 114 Processing sheet with id=AA1, first strand: chain 'B' and resid 18 through 23 Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 60 removed outlier: 5.308A pdb=" N PHE B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ARG B 38 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N CYS B 96 " --> pdb=" O GLY B 118 " (cutoff:3.500A) 281 hydrogen bonds defined for protein. 810 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.58 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 4724 1.04 - 1.24: 632 1.24 - 1.44: 1489 1.44 - 1.64: 2676 1.64 - 1.84: 55 Bond restraints: 9576 Sorted by residual: bond pdb=" C ALA A 104 " pdb=" N ASP A 105 " ideal model delta sigma weight residual 1.335 1.287 0.048 1.36e-02 5.41e+03 1.26e+01 bond pdb=" N25 CXN A 801 " pdb=" O24 CXN A 801 " ideal model delta sigma weight residual 1.363 1.416 -0.053 2.00e-02 2.50e+03 7.05e+00 bond pdb=" N ASP A 105 " pdb=" H ASP A 105 " ideal model delta sigma weight residual 0.860 0.912 -0.052 2.00e-02 2.50e+03 6.70e+00 bond pdb=" C6 CXN A 801 " pdb=" C8 CXN A 801 " ideal model delta sigma weight residual 1.546 1.507 0.039 2.00e-02 2.50e+03 3.80e+00 bond pdb=" C ASP A 105 " pdb=" O ASP A 105 " ideal model delta sigma weight residual 1.237 1.214 0.023 1.19e-02 7.06e+03 3.61e+00 ... (remaining 9571 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 17141 1.97 - 3.94: 138 3.94 - 5.91: 12 5.91 - 7.88: 0 7.88 - 9.84: 2 Bond angle restraints: 17293 Sorted by residual: angle pdb=" CA ASP A 105 " pdb=" C ASP A 105 " pdb=" O ASP A 105 " ideal model delta sigma weight residual 120.42 116.81 3.61 1.06e+00 8.90e-01 1.16e+01 angle pdb=" C21 CXN A 801 " pdb=" C22 CXN A 801 " pdb=" C26 CXN A 801 " ideal model delta sigma weight residual 132.03 122.19 9.84 3.00e+00 1.11e-01 1.08e+01 angle pdb=" C ALA A 104 " pdb=" N ASP A 105 " pdb=" CA ASP A 105 " ideal model delta sigma weight residual 120.29 124.57 -4.28 1.42e+00 4.96e-01 9.10e+00 angle pdb=" C21 CXN A 801 " pdb=" C22 CXN A 801 " pdb=" C23 CXN A 801 " ideal model delta sigma weight residual 124.59 133.26 -8.67 3.00e+00 1.11e-01 8.35e+00 angle pdb=" N THR A 96 " pdb=" CA THR A 96 " pdb=" C THR A 96 " ideal model delta sigma weight residual 109.81 115.47 -5.66 2.21e+00 2.05e-01 6.57e+00 ... (remaining 17288 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.03: 4246 27.03 - 54.06: 244 54.06 - 81.08: 44 81.08 - 108.11: 3 108.11 - 135.14: 4 Dihedral angle restraints: 4541 sinusoidal: 2402 harmonic: 2139 Sorted by residual: dihedral pdb=" CA TRP A 283 " pdb=" C TRP A 283 " pdb=" N ALA A 284 " pdb=" CA ALA A 284 " ideal model delta harmonic sigma weight residual 180.00 157.35 22.65 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA GLY A 159 " pdb=" C GLY A 159 " pdb=" N ILE A 160 " pdb=" CA ILE A 160 " ideal model delta harmonic sigma weight residual 180.00 157.36 22.64 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" C52 CXN A 801 " pdb=" C5 CXN A 801 " pdb=" C6 CXN A 801 " pdb=" N7 CXN A 801 " ideal model delta sinusoidal sigma weight residual 144.67 -80.19 -135.14 1 3.00e+01 1.11e-03 1.82e+01 ... (remaining 4538 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 484 0.029 - 0.057: 168 0.057 - 0.086: 57 0.086 - 0.114: 21 0.114 - 0.143: 8 Chirality restraints: 738 Sorted by residual: chirality pdb=" CA ILE A 133 " pdb=" N ILE A 133 " pdb=" C ILE A 133 " pdb=" CB ILE A 133 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.11e-01 chirality pdb=" CA PRO A 97 " pdb=" N PRO A 97 " pdb=" C PRO A 97 " pdb=" CB PRO A 97 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA ILE A 601 " pdb=" N ILE A 601 " pdb=" C ILE A 601 " pdb=" CB ILE A 601 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.96e-01 ... (remaining 735 not shown) Planarity restraints: 1381 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 CXN A 801 " 0.191 2.00e-02 2.50e+03 1.65e-01 3.41e+02 pdb=" C21 CXN A 801 " -0.042 2.00e-02 2.50e+03 pdb=" C22 CXN A 801 " -0.028 2.00e-02 2.50e+03 pdb=" N2 CXN A 801 " -0.273 2.00e-02 2.50e+03 pdb=" O21 CXN A 801 " 0.151 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C21 CXN A 801 " 0.050 2.00e-02 2.50e+03 3.67e-02 2.70e+01 pdb=" C22 CXN A 801 " -0.015 2.00e-02 2.50e+03 pdb=" C23 CXN A 801 " 0.016 2.00e-02 2.50e+03 pdb=" C26 CXN A 801 " -0.010 2.00e-02 2.50e+03 pdb=" C27 CXN A 801 " -0.058 2.00e-02 2.50e+03 pdb=" C28 CXN A 801 " -0.046 2.00e-02 2.50e+03 pdb=" N25 CXN A 801 " 0.023 2.00e-02 2.50e+03 pdb=" O24 CXN A 801 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 87 " 0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO B 88 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 88 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 88 " 0.027 5.00e-02 4.00e+02 ... (remaining 1378 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 1029 2.23 - 2.83: 20711 2.83 - 3.42: 24832 3.42 - 4.01: 33869 4.01 - 4.60: 52356 Nonbonded interactions: 132797 Sorted by model distance: nonbonded pdb=" O TRP B 53 " pdb=" HG SER B 54 " model vdw 1.642 2.450 nonbonded pdb=" O ALA A 637 " pdb=" HZ3 LYS A 642 " model vdw 1.659 2.450 nonbonded pdb=" OD1 ASP A 170 " pdb=" HH TYR A 634 " model vdw 1.670 2.450 nonbonded pdb=" O PHE A 167 " pdb="HE21 GLN A 171 " model vdw 1.676 2.450 nonbonded pdb=" OD1 ASP A 333 " pdb=" H LEU A 334 " model vdw 1.678 2.450 ... (remaining 132792 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: 5.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.150 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 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 : 0.003 0.053 4844 Z= 0.153 Angle : 0.603 9.844 6587 Z= 0.321 Chirality : 0.037 0.143 738 Planarity : 0.007 0.165 814 Dihedral : 18.476 135.140 1725 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 1.60 % Allowed : 24.40 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.36), residues: 589 helix: 1.20 (0.29), residues: 343 sheet: -1.84 (0.65), residues: 59 loop : -1.72 (0.45), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 101 TYR 0.010 0.001 TYR A 183 PHE 0.008 0.001 PHE A 48 TRP 0.009 0.001 TRP A 107 HIS 0.009 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 4842) covalent geometry : angle 0.60264 ( 6583) SS BOND : bond 0.00234 ( 2) SS BOND : angle 1.26176 ( 4) hydrogen bonds : bond 0.16297 ( 281) hydrogen bonds : angle 6.41179 ( 810) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 GLN cc_start: 0.7524 (mm-40) cc_final: 0.7198 (mt0) outliers start: 8 outliers final: 7 residues processed: 79 average time/residue: 0.1409 time to fit residues: 14.4432 Evaluate side-chains 77 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 607 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.2980 chunk 25 optimal weight: 0.2980 chunk 58 optimal weight: 0.2980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.165640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.138550 restraints weight = 14854.177| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.61 r_work: 0.3391 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.0618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4844 Z= 0.135 Angle : 0.563 5.794 6587 Z= 0.294 Chirality : 0.038 0.153 738 Planarity : 0.004 0.047 814 Dihedral : 11.746 130.555 687 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 1.80 % Allowed : 24.20 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.36), residues: 589 helix: 1.64 (0.28), residues: 345 sheet: -2.21 (0.62), residues: 59 loop : -1.78 (0.45), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 322 TYR 0.013 0.001 TYR A 634 PHE 0.016 0.001 PHE A 48 TRP 0.006 0.001 TRP A 107 HIS 0.009 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 4842) covalent geometry : angle 0.56204 ( 6583) SS BOND : bond 0.00236 ( 2) SS BOND : angle 1.49277 ( 4) hydrogen bonds : bond 0.04630 ( 281) hydrogen bonds : angle 4.43121 ( 810) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: B 112 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7267 (pm20) outliers start: 9 outliers final: 7 residues processed: 70 average time/residue: 0.1552 time to fit residues: 14.2431 Evaluate side-chains 72 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 112 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 21 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 12 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.163700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.136523 restraints weight = 15018.112| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.63 r_work: 0.3333 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.0834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4844 Z= 0.171 Angle : 0.569 5.350 6587 Z= 0.297 Chirality : 0.039 0.151 738 Planarity : 0.004 0.050 814 Dihedral : 11.635 138.863 680 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 1.80 % Allowed : 23.40 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.35), residues: 589 helix: 1.60 (0.28), residues: 346 sheet: -2.06 (0.62), residues: 57 loop : -1.94 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 322 TYR 0.014 0.001 TYR A 634 PHE 0.022 0.001 PHE A 48 TRP 0.010 0.001 TRP A 107 HIS 0.008 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 4842) covalent geometry : angle 0.56781 ( 6583) SS BOND : bond 0.00209 ( 2) SS BOND : angle 1.66290 ( 4) hydrogen bonds : bond 0.04777 ( 281) hydrogen bonds : angle 4.35623 ( 810) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.156 Fit side-chains revert: symmetry clash REVERT: B 112 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7274 (pm20) outliers start: 9 outliers final: 6 residues processed: 71 average time/residue: 0.1562 time to fit residues: 14.3533 Evaluate side-chains 70 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 112 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 30 optimal weight: 3.9990 chunk 0 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.163109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.135861 restraints weight = 15026.094| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.63 r_work: 0.3341 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4844 Z= 0.172 Angle : 0.564 5.184 6587 Z= 0.296 Chirality : 0.039 0.149 738 Planarity : 0.004 0.047 814 Dihedral : 11.341 137.320 676 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.40 % Allowed : 23.00 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.35), residues: 589 helix: 1.61 (0.28), residues: 346 sheet: -2.07 (0.63), residues: 57 loop : -1.95 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 322 TYR 0.013 0.001 TYR A 634 PHE 0.020 0.001 PHE A 48 TRP 0.010 0.001 TRP A 107 HIS 0.008 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 4842) covalent geometry : angle 0.56309 ( 6583) SS BOND : bond 0.00176 ( 2) SS BOND : angle 1.70762 ( 4) hydrogen bonds : bond 0.04586 ( 281) hydrogen bonds : angle 4.29455 ( 810) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 112 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7291 (pm20) outliers start: 12 outliers final: 9 residues processed: 70 average time/residue: 0.1491 time to fit residues: 13.6257 Evaluate side-chains 74 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 112 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 0.0980 chunk 37 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.163073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.134983 restraints weight = 14897.055| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.67 r_work: 0.3331 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4844 Z= 0.138 Angle : 0.540 4.942 6587 Z= 0.283 Chirality : 0.038 0.148 738 Planarity : 0.004 0.046 814 Dihedral : 11.276 136.403 676 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 2.20 % Allowed : 23.00 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.36), residues: 589 helix: 1.74 (0.28), residues: 346 sheet: -2.02 (0.64), residues: 57 loop : -1.93 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 322 TYR 0.012 0.001 TYR A 634 PHE 0.017 0.001 PHE A 48 TRP 0.009 0.001 TRP A 107 HIS 0.007 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 4842) covalent geometry : angle 0.53890 ( 6583) SS BOND : bond 0.00135 ( 2) SS BOND : angle 1.63569 ( 4) hydrogen bonds : bond 0.04192 ( 281) hydrogen bonds : angle 4.18529 ( 810) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: B 45 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.8082 (ttp-170) REVERT: B 112 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7285 (pm20) outliers start: 11 outliers final: 8 residues processed: 70 average time/residue: 0.1480 time to fit residues: 13.2102 Evaluate side-chains 70 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 112 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 7 optimal weight: 0.2980 chunk 20 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 31 optimal weight: 0.0770 chunk 22 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.165006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.138120 restraints weight = 14887.117| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.60 r_work: 0.3356 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4844 Z= 0.133 Angle : 0.533 4.918 6587 Z= 0.280 Chirality : 0.038 0.147 738 Planarity : 0.004 0.046 814 Dihedral : 11.255 136.066 676 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.60 % Allowed : 22.80 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.36), residues: 589 helix: 1.80 (0.28), residues: 346 sheet: -2.01 (0.64), residues: 57 loop : -1.93 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 266 TYR 0.012 0.001 TYR A 634 PHE 0.016 0.001 PHE A 48 TRP 0.008 0.001 TRP A 107 HIS 0.007 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 4842) covalent geometry : angle 0.53131 ( 6583) SS BOND : bond 0.00132 ( 2) SS BOND : angle 1.63005 ( 4) hydrogen bonds : bond 0.04052 ( 281) hydrogen bonds : angle 4.12329 ( 810) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: B 45 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.8028 (ttp-170) REVERT: B 112 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7287 (pm20) outliers start: 13 outliers final: 8 residues processed: 70 average time/residue: 0.1428 time to fit residues: 12.9526 Evaluate side-chains 72 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 112 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 45 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.161866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.134609 restraints weight = 14932.189| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.61 r_work: 0.3325 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 4844 Z= 0.197 Angle : 0.579 5.254 6587 Z= 0.305 Chirality : 0.040 0.151 738 Planarity : 0.005 0.049 814 Dihedral : 11.353 137.646 676 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 2.40 % Allowed : 23.00 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.35), residues: 589 helix: 1.60 (0.28), residues: 344 sheet: -2.07 (0.63), residues: 57 loop : -1.94 (0.43), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 266 TYR 0.014 0.002 TYR A 634 PHE 0.022 0.002 PHE A 48 TRP 0.011 0.001 TRP A 107 HIS 0.007 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00471 ( 4842) covalent geometry : angle 0.57693 ( 6583) SS BOND : bond 0.00169 ( 2) SS BOND : angle 1.85257 ( 4) hydrogen bonds : bond 0.04727 ( 281) hydrogen bonds : angle 4.26459 ( 810) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: A 404 MET cc_start: 0.4766 (OUTLIER) cc_final: 0.3295 (pmm) REVERT: B 45 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.8039 (ttp-170) REVERT: B 112 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7302 (pm20) outliers start: 12 outliers final: 9 residues processed: 71 average time/residue: 0.1748 time to fit residues: 15.9831 Evaluate side-chains 75 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 112 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 44 optimal weight: 0.4980 chunk 26 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.162882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.135564 restraints weight = 15016.627| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.63 r_work: 0.3338 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4844 Z= 0.161 Angle : 0.553 5.042 6587 Z= 0.291 Chirality : 0.038 0.149 738 Planarity : 0.005 0.048 814 Dihedral : 11.318 135.864 676 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 3.40 % Allowed : 22.00 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.35), residues: 589 helix: 1.62 (0.28), residues: 346 sheet: -2.09 (0.63), residues: 57 loop : -1.90 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 266 TYR 0.012 0.001 TYR A 634 PHE 0.019 0.001 PHE A 48 TRP 0.010 0.001 TRP A 107 HIS 0.006 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 4842) covalent geometry : angle 0.55116 ( 6583) SS BOND : bond 0.00153 ( 2) SS BOND : angle 1.75447 ( 4) hydrogen bonds : bond 0.04380 ( 281) hydrogen bonds : angle 4.19999 ( 810) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: A 311 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8127 (mmm) REVERT: A 404 MET cc_start: 0.4690 (OUTLIER) cc_final: 0.3268 (pmm) REVERT: B 45 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.8029 (ttp-170) REVERT: B 112 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7273 (pm20) outliers start: 17 outliers final: 11 residues processed: 70 average time/residue: 0.1691 time to fit residues: 15.3007 Evaluate side-chains 76 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 124 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 55 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 44 optimal weight: 0.1980 chunk 1 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.162776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.135684 restraints weight = 14921.076| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.61 r_work: 0.3341 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4844 Z= 0.160 Angle : 0.552 5.035 6587 Z= 0.291 Chirality : 0.038 0.149 738 Planarity : 0.005 0.050 814 Dihedral : 11.301 136.090 676 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 3.20 % Allowed : 22.00 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.35), residues: 589 helix: 1.64 (0.28), residues: 346 sheet: -2.07 (0.63), residues: 57 loop : -1.93 (0.43), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 266 TYR 0.013 0.001 TYR A 634 PHE 0.018 0.001 PHE A 48 TRP 0.010 0.001 TRP A 107 HIS 0.006 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 4842) covalent geometry : angle 0.55055 ( 6583) SS BOND : bond 0.00152 ( 2) SS BOND : angle 1.74437 ( 4) hydrogen bonds : bond 0.04336 ( 281) hydrogen bonds : angle 4.18221 ( 810) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 311 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.8111 (mmm) REVERT: A 404 MET cc_start: 0.4694 (OUTLIER) cc_final: 0.3312 (pmm) REVERT: B 45 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.8026 (ttp-170) REVERT: B 112 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7285 (pm20) outliers start: 16 outliers final: 11 residues processed: 72 average time/residue: 0.1486 time to fit residues: 13.9046 Evaluate side-chains 77 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 124 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 15 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 54 optimal weight: 0.0470 chunk 45 optimal weight: 0.9980 chunk 33 optimal weight: 0.1980 chunk 14 optimal weight: 0.4980 chunk 52 optimal weight: 1.9990 chunk 58 optimal weight: 0.0870 chunk 25 optimal weight: 0.4980 overall best weight: 0.2656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.165979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.138138 restraints weight = 14807.495| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.67 r_work: 0.3356 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4844 Z= 0.105 Angle : 0.517 4.677 6587 Z= 0.272 Chirality : 0.037 0.145 738 Planarity : 0.004 0.047 814 Dihedral : 11.202 133.871 676 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.20 % Allowed : 22.60 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.36), residues: 589 helix: 1.94 (0.28), residues: 345 sheet: -2.03 (0.63), residues: 57 loop : -1.83 (0.43), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 266 TYR 0.010 0.001 TYR A 634 PHE 0.012 0.001 PHE A 48 TRP 0.008 0.001 TRP A 280 HIS 0.006 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 4842) covalent geometry : angle 0.51530 ( 6583) SS BOND : bond 0.00158 ( 2) SS BOND : angle 1.57060 ( 4) hydrogen bonds : bond 0.03653 ( 281) hydrogen bonds : angle 4.01596 ( 810) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 311 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8122 (mmm) REVERT: B 112 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7268 (pm20) outliers start: 11 outliers final: 7 residues processed: 68 average time/residue: 0.1838 time to fit residues: 16.1064 Evaluate side-chains 69 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 112 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 48 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 23 optimal weight: 0.0060 chunk 0 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 26 optimal weight: 0.3980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.164681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.137739 restraints weight = 14856.228| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.61 r_work: 0.3356 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4844 Z= 0.133 Angle : 0.528 4.851 6587 Z= 0.278 Chirality : 0.038 0.148 738 Planarity : 0.005 0.048 814 Dihedral : 11.207 135.405 676 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 2.60 % Allowed : 22.00 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.36), residues: 589 helix: 1.88 (0.28), residues: 345 sheet: -2.04 (0.63), residues: 57 loop : -1.83 (0.43), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 266 TYR 0.013 0.001 TYR A 634 PHE 0.015 0.001 PHE A 48 TRP 0.008 0.001 TRP A 107 HIS 0.006 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 4842) covalent geometry : angle 0.52689 ( 6583) SS BOND : bond 0.00139 ( 2) SS BOND : angle 1.67898 ( 4) hydrogen bonds : bond 0.03942 ( 281) hydrogen bonds : angle 4.03220 ( 810) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2813.24 seconds wall clock time: 48 minutes 22.89 seconds (2902.89 seconds total)