Starting phenix.real_space_refine on Mon May 12 23:28:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bit_44601/05_2025/9bit_44601_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bit_44601/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9bit_44601/05_2025/9bit_44601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bit_44601/05_2025/9bit_44601.map" model { file = "/net/cci-nas-00/data/ceres_data/9bit_44601/05_2025/9bit_44601_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bit_44601/05_2025/9bit_44601_trim.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.69, per 1000 atoms: 0.60 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: 2.36 Conformation dependent library (CDL) restraints added in 585.4 milliseconds 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: 0.61 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: 3.12 Time building geometry restraints manager: 2.82 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: 9.700 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: 0.170 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.260 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.330 ------------------------------------------------------------------------------- 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 : 6.13 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (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 TRP 0.009 0.001 TRP A 107 HIS 0.009 0.001 HIS A 291 PHE 0.008 0.001 PHE A 48 TYR 0.010 0.001 TYR A 183 ARG 0.002 0.000 ARG B 101 Details of bonding type rmsd hydrogen bonds : bond 0.16297 ( 281) hydrogen bonds : angle 6.41179 ( 810) SS BOND : bond 0.00234 ( 2) SS BOND : angle 1.26176 ( 4) covalent geometry : bond 0.00319 ( 4842) covalent geometry : angle 0.60264 ( 6583) *********************** 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 : 0.743 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: 0.3448 time to fit residues: 35.4236 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 : 0.748 ------------------------------------------------------------------------------- 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 49 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 17 optimal weight: 0.0770 chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 53 optimal weight: 0.0970 overall best weight: 0.5536 ------------------------------------------------------------------------------- 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 = 0.3850 r_free = 0.3850 target = 0.164849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.137697 restraints weight = 14864.718| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.61 r_work: 0.3351 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.0612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4844 Z= 0.147 Angle : 0.570 5.551 6587 Z= 0.298 Chirality : 0.038 0.153 738 Planarity : 0.004 0.047 814 Dihedral : 11.783 131.575 687 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.36), residues: 589 helix: 1.58 (0.28), residues: 345 sheet: -2.23 (0.61), residues: 59 loop : -1.78 (0.45), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 107 HIS 0.009 0.001 HIS A 291 PHE 0.017 0.001 PHE A 48 TYR 0.014 0.001 TYR A 634 ARG 0.004 0.000 ARG A 322 Details of bonding type rmsd hydrogen bonds : bond 0.04836 ( 281) hydrogen bonds : angle 4.46454 ( 810) SS BOND : bond 0.00206 ( 2) SS BOND : angle 1.53031 ( 4) covalent geometry : bond 0.00340 ( 4842) covalent geometry : angle 0.56847 ( 6583) *********************** 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 74 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: B 112 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7304 (pm20) outliers start: 9 outliers final: 7 residues processed: 69 average time/residue: 0.3455 time to fit residues: 31.0811 Evaluate side-chains 71 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.678 ------------------------------------------------------------------------------- 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 38 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 48 optimal weight: 0.0030 chunk 18 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 41 optimal weight: 0.2980 chunk 24 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 overall best weight: 0.5990 ------------------------------------------------------------------------------- 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 = 0.3847 r_free = 0.3847 target = 0.164782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.137761 restraints weight = 14970.205| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.62 r_work: 0.3374 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.0846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4844 Z= 0.145 Angle : 0.550 5.146 6587 Z= 0.287 Chirality : 0.038 0.150 738 Planarity : 0.004 0.049 814 Dihedral : 11.596 138.430 680 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 4.33 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.36), residues: 589 helix: 1.71 (0.28), residues: 346 sheet: -2.18 (0.62), residues: 59 loop : -1.86 (0.45), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.009 0.001 HIS A 291 PHE 0.019 0.001 PHE A 48 TYR 0.012 0.001 TYR A 634 ARG 0.003 0.000 ARG A 322 Details of bonding type rmsd hydrogen bonds : bond 0.04462 ( 281) hydrogen bonds : angle 4.28180 ( 810) SS BOND : bond 0.00157 ( 2) SS BOND : angle 1.57487 ( 4) covalent geometry : bond 0.00337 ( 4842) covalent geometry : angle 0.54859 ( 6583) *********************** 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 : 0.701 Fit side-chains revert: symmetry clash REVERT: B 112 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7245 (pm20) outliers start: 9 outliers final: 6 residues processed: 71 average time/residue: 0.3365 time to fit residues: 31.4421 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 : 0.755 ------------------------------------------------------------------------------- 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 23 optimal weight: 0.0870 chunk 41 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 56 optimal weight: 0.4980 chunk 53 optimal weight: 0.1980 chunk 6 optimal weight: 0.9990 chunk 46 optimal weight: 0.2980 chunk 15 optimal weight: 0.9990 overall best weight: 0.3358 ------------------------------------------------------------------------------- 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 = 0.3869 r_free = 0.3869 target = 0.166863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.139988 restraints weight = 14766.272| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.61 r_work: 0.3380 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1047 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= 0.111 Angle : 0.518 4.817 6587 Z= 0.271 Chirality : 0.037 0.149 738 Planarity : 0.004 0.046 814 Dihedral : 11.187 135.261 676 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.36), residues: 589 helix: 2.04 (0.29), residues: 339 sheet: -2.07 (0.64), residues: 59 loop : -1.63 (0.45), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 280 HIS 0.007 0.001 HIS A 291 PHE 0.013 0.001 PHE A 48 TYR 0.010 0.001 TYR A 634 ARG 0.002 0.000 ARG A 266 Details of bonding type rmsd hydrogen bonds : bond 0.03804 ( 281) hydrogen bonds : angle 4.09275 ( 810) SS BOND : bond 0.00127 ( 2) SS BOND : angle 1.49382 ( 4) covalent geometry : bond 0.00249 ( 4842) covalent geometry : angle 0.51694 ( 6583) *********************** 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 75 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.634 Fit side-chains revert: symmetry clash REVERT: B 79 MET cc_start: 0.8545 (ttp) cc_final: 0.8344 (ttp) REVERT: B 112 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7209 (pm20) outliers start: 11 outliers final: 8 residues processed: 70 average time/residue: 0.3452 time to fit residues: 31.2008 Evaluate side-chains 71 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 316 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 0.0980 chunk 2 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3849 r_free = 0.3849 target = 0.164985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.137884 restraints weight = 14850.733| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.62 r_work: 0.3320 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1093 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= 0.153 Angle : 0.544 5.003 6587 Z= 0.285 Chirality : 0.038 0.149 738 Planarity : 0.004 0.047 814 Dihedral : 11.235 137.317 676 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 2.20 % Allowed : 22.80 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.36), residues: 589 helix: 1.85 (0.28), residues: 342 sheet: -1.94 (0.65), residues: 57 loop : -1.67 (0.45), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 107 HIS 0.008 0.001 HIS A 291 PHE 0.018 0.001 PHE A 48 TYR 0.014 0.001 TYR A 634 ARG 0.009 0.000 ARG A 266 Details of bonding type rmsd hydrogen bonds : bond 0.04243 ( 281) hydrogen bonds : angle 4.13031 ( 810) SS BOND : bond 0.00138 ( 2) SS BOND : angle 1.69401 ( 4) covalent geometry : bond 0.00361 ( 4842) covalent geometry : angle 0.54294 ( 6583) *********************** 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 73 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.735 Fit side-chains revert: symmetry clash REVERT: A 311 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.8182 (mmm) REVERT: B 45 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.8052 (ttp-170) REVERT: B 112 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7273 (pm20) outliers start: 11 outliers final: 8 residues processed: 68 average time/residue: 0.3429 time to fit residues: 30.5498 Evaluate side-chains 72 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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 311 MET Chi-restraints excluded: chain A residue 316 LEU 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 36 optimal weight: 0.5980 chunk 43 optimal weight: 0.4980 chunk 41 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 38 optimal weight: 0.1980 chunk 3 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3855 r_free = 0.3855 target = 0.165598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.138660 restraints weight = 14855.602| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.60 r_work: 0.3368 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1175 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= 0.128 Angle : 0.524 4.843 6587 Z= 0.275 Chirality : 0.037 0.149 738 Planarity : 0.004 0.047 814 Dihedral : 11.195 135.547 676 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.60 % Allowed : 22.40 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.36), residues: 589 helix: 1.90 (0.28), residues: 345 sheet: -1.93 (0.65), residues: 57 loop : -1.90 (0.44), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 107 HIS 0.002 0.001 HIS A 291 PHE 0.016 0.001 PHE A 48 TYR 0.011 0.001 TYR A 634 ARG 0.006 0.000 ARG A 266 Details of bonding type rmsd hydrogen bonds : bond 0.03963 ( 281) hydrogen bonds : angle 4.06659 ( 810) SS BOND : bond 0.00151 ( 2) SS BOND : angle 1.59498 ( 4) covalent geometry : bond 0.00295 ( 4842) covalent geometry : angle 0.52249 ( 6583) *********************** 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 75 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: A 311 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.8116 (mmm) REVERT: B 45 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.8014 (ttp-170) REVERT: B 112 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7240 (pm20) outliers start: 13 outliers final: 9 residues processed: 70 average time/residue: 0.3501 time to fit residues: 32.2783 Evaluate side-chains 74 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.705 ------------------------------------------------------------------------------- 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 316 LEU 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 1 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 chunk 33 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.163412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.136222 restraints weight = 15009.946| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.62 r_work: 0.3331 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4844 Z= 0.172 Angle : 0.557 5.128 6587 Z= 0.293 Chirality : 0.039 0.150 738 Planarity : 0.005 0.048 814 Dihedral : 11.263 136.838 676 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 2.80 % Allowed : 22.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.36), residues: 589 helix: 1.69 (0.28), residues: 346 sheet: -2.01 (0.64), residues: 57 loop : -1.87 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.003 0.001 HIS A 291 PHE 0.020 0.001 PHE A 48 TYR 0.013 0.001 TYR A 634 ARG 0.005 0.000 ARG A 266 Details of bonding type rmsd hydrogen bonds : bond 0.04462 ( 281) hydrogen bonds : angle 4.16505 ( 810) SS BOND : bond 0.00167 ( 2) SS BOND : angle 1.76543 ( 4) covalent geometry : bond 0.00409 ( 4842) covalent geometry : angle 0.55531 ( 6583) *********************** 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 76 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: B 45 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.8050 (ttp-170) REVERT: B 112 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7277 (pm20) outliers start: 14 outliers final: 10 residues processed: 70 average time/residue: 0.3902 time to fit residues: 34.6974 Evaluate side-chains 73 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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 316 LEU Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 657 ASN 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 49 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 46 optimal weight: 0.4980 chunk 51 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 31 optimal weight: 0.4980 chunk 24 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 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 = 0.3819 r_free = 0.3819 target = 0.162421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.134050 restraints weight = 15209.393| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.71 r_work: 0.3333 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1287 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= 0.157 Angle : 0.547 5.011 6587 Z= 0.288 Chirality : 0.038 0.150 738 Planarity : 0.005 0.047 814 Dihedral : 11.259 135.590 676 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 3.00 % Allowed : 22.00 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.36), residues: 589 helix: 1.72 (0.28), residues: 346 sheet: -2.01 (0.63), residues: 57 loop : -1.86 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.003 0.001 HIS A 291 PHE 0.019 0.001 PHE A 48 TYR 0.012 0.001 TYR A 634 ARG 0.007 0.000 ARG A 266 Details of bonding type rmsd hydrogen bonds : bond 0.04283 ( 281) hydrogen bonds : angle 4.14071 ( 810) SS BOND : bond 0.00144 ( 2) SS BOND : angle 1.71455 ( 4) covalent geometry : bond 0.00369 ( 4842) covalent geometry : angle 0.54574 ( 6583) *********************** 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 80 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.743 Fit side-chains revert: symmetry clash REVERT: A 311 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.8151 (mmm) REVERT: B 45 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.8032 (ttp-170) REVERT: B 112 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7242 (pm20) outliers start: 15 outliers final: 10 residues processed: 71 average time/residue: 0.3546 time to fit residues: 32.7778 Evaluate side-chains 76 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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 316 LEU Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 657 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 4 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 37 optimal weight: 0.4980 chunk 16 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 9 optimal weight: 0.3980 chunk 33 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3837 r_free = 0.3837 target = 0.163897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.136891 restraints weight = 14884.446| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.60 r_work: 0.3350 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1319 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= 0.148 Angle : 0.542 4.942 6587 Z= 0.286 Chirality : 0.038 0.150 738 Planarity : 0.005 0.047 814 Dihedral : 11.238 135.399 676 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 3.00 % Allowed : 22.00 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.36), residues: 589 helix: 1.78 (0.28), residues: 345 sheet: -1.95 (0.64), residues: 57 loop : -1.83 (0.44), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.003 0.001 HIS A 291 PHE 0.017 0.001 PHE A 48 TYR 0.012 0.001 TYR A 634 ARG 0.008 0.000 ARG A 266 Details of bonding type rmsd hydrogen bonds : bond 0.04164 ( 281) hydrogen bonds : angle 4.10995 ( 810) SS BOND : bond 0.00131 ( 2) SS BOND : angle 1.70253 ( 4) covalent geometry : bond 0.00346 ( 4842) covalent geometry : angle 0.54079 ( 6583) *********************** 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 77 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8155 (mmm) REVERT: B 112 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7246 (pm20) outliers start: 15 outliers final: 11 residues processed: 69 average time/residue: 0.3512 time to fit residues: 31.6264 Evaluate side-chains 75 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 316 LEU Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 657 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 19 optimal weight: 0.9980 chunk 7 optimal weight: 0.3980 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 41 optimal weight: 0.0980 chunk 49 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 54 optimal weight: 0.3980 chunk 2 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.3861 r_free = 0.3861 target = 0.166139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.139098 restraints weight = 14975.905| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.61 r_work: 0.3347 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4844 Z= 0.121 Angle : 0.520 4.752 6587 Z= 0.273 Chirality : 0.037 0.148 738 Planarity : 0.004 0.045 814 Dihedral : 11.178 134.351 676 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.40 % Allowed : 22.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.36), residues: 589 helix: 1.93 (0.28), residues: 345 sheet: -1.99 (0.64), residues: 57 loop : -1.84 (0.43), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 107 HIS 0.002 0.001 HIS A 291 PHE 0.014 0.001 PHE A 48 TYR 0.011 0.001 TYR A 634 ARG 0.007 0.000 ARG A 266 Details of bonding type rmsd hydrogen bonds : bond 0.03796 ( 281) hydrogen bonds : angle 3.99651 ( 810) SS BOND : bond 0.00142 ( 2) SS BOND : angle 1.63068 ( 4) covalent geometry : bond 0.00276 ( 4842) covalent geometry : angle 0.51868 ( 6583) ********************** 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 75 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.664 Fit side-chains revert: symmetry clash REVERT: A 311 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.8131 (mmm) REVERT: B 112 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7279 (pm20) outliers start: 12 outliers final: 8 residues processed: 70 average time/residue: 0.3733 time to fit residues: 34.1927 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 : 0.707 ------------------------------------------------------------------------------- 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 316 LEU 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 35 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 37 optimal weight: 0.3980 chunk 54 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 48 optimal weight: 0.3980 chunk 22 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 13 optimal weight: 0.0050 chunk 38 optimal weight: 0.5980 chunk 34 optimal weight: 0.4980 overall best weight: 0.3794 ------------------------------------------------------------------------------- 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 = 0.3863 r_free = 0.3863 target = 0.166407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.138558 restraints weight = 14938.016| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.67 r_work: 0.3376 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4844 Z= 0.115 Angle : 0.515 4.728 6587 Z= 0.271 Chirality : 0.037 0.148 738 Planarity : 0.004 0.043 814 Dihedral : 11.142 134.390 676 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.00 % Allowed : 22.40 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.36), residues: 589 helix: 1.98 (0.28), residues: 345 sheet: -2.00 (0.64), residues: 57 loop : -1.82 (0.43), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 280 HIS 0.003 0.000 HIS A 291 PHE 0.013 0.001 PHE A 48 TYR 0.012 0.001 TYR A 634 ARG 0.007 0.000 ARG A 266 Details of bonding type rmsd hydrogen bonds : bond 0.03720 ( 281) hydrogen bonds : angle 3.95877 ( 810) SS BOND : bond 0.00143 ( 2) SS BOND : angle 1.60461 ( 4) covalent geometry : bond 0.00262 ( 4842) covalent geometry : angle 0.51364 ( 6583) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5633.09 seconds wall clock time: 97 minutes 39.63 seconds (5859.63 seconds total)