Starting phenix.real_space_refine on Thu Oct 22 18:58:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wn1_32619/10_2026/7wn1_32619.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wn1_32619/10_2026/7wn1_32619.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7wn1_32619/10_2026/7wn1_32619.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wn1_32619/10_2026/7wn1_32619.cif" model { file = "/net/cci-nas-00/data/ceres_data/7wn1_32619/10_2026/7wn1_32619.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wn1_32619/10_2026/7wn1_32619.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wn1_32619/10_2026/7wn1_32619.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wn1_32619/10_2026/7wn1_32619.map" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 2572 2.51 5 N 616 2.21 5 O 687 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3901 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2953 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 11, 'TRANS': 359} Chain breaks: 1 Chain: "C" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 929 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'NOS%rna2p': 1} Classifications: {'undetermined': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 1.59, per 1000 atoms: 0.41 Number of scatterers: 3901 At special positions: 0 Unit cell: (110.39, 60.59, 64.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 687 8.00 N 616 7.00 C 2572 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " 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: 0.32 Conformation dependent library (CDL) restraints added in 108.8 milliseconds 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 914 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 3 sheets defined 64.3% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 31 through 59 removed outlier: 4.331A pdb=" N VAL A 52 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N TRP A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 83 removed outlier: 3.547A pdb=" N ASN A 66 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE A 82 " --> pdb=" O ILE A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 88 No H-bonds generated for 'chain 'A' and resid 86 through 88' Processing helix chain 'A' and resid 89 through 111 Processing helix chain 'A' and resid 112 through 144 Processing helix chain 'A' and resid 149 through 175 removed outlier: 3.802A pdb=" N GLN A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N PHE A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 210 Processing helix chain 'A' and resid 231 through 239 Processing helix chain 'A' and resid 239 through 257 removed outlier: 3.734A pdb=" N ILE A 243 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN A 250 " --> pdb=" O MET A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 270 removed outlier: 3.674A pdb=" N GLN A 266 " --> pdb=" O HIS A 262 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 290 removed outlier: 3.759A pdb=" N THR A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 278 " --> pdb=" O TYR A 274 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE A 288 " --> pdb=" O GLN A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 296 removed outlier: 3.967A pdb=" N ASN A 295 " --> pdb=" O ARG A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 319 Processing helix chain 'A' and resid 321 through 332 removed outlier: 3.538A pdb=" N TRP A 325 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA A 330 " --> pdb=" O PHE A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 369 removed outlier: 3.804A pdb=" N LEU A 350 " --> pdb=" O CYS A 346 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) Proline residue: A 361 - end of helix removed outlier: 5.181A pdb=" N VAL A 366 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N LYS A 367 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 400 removed outlier: 3.655A pdb=" N ILE A 378 " --> pdb=" O LYS A 374 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR A 400 " --> pdb=" O GLY A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 405 Processing helix chain 'C' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.193A pdb=" N GLY C 10 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ARG C 38 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LEU C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.193A pdb=" N GLY C 10 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN C 109 " --> pdb=" O THR C 99 " (cutoff:3.500A) 260 hydrogen bonds defined for protein. 750 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: 1.24 Time building geometry restraints manager: 0.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 823 1.33 - 1.45: 929 1.45 - 1.57: 2205 1.57 - 1.69: 2 1.69 - 1.81: 39 Bond restraints: 3998 Sorted by residual: bond pdb=" C1' NOS A 501 " pdb=" O4' NOS A 501 " ideal model delta sigma weight residual 1.415 1.600 -0.185 1.50e-02 4.44e+03 1.53e+02 bond pdb=" C1' NOS A 501 " pdb=" C2' NOS A 501 " ideal model delta sigma weight residual 1.526 1.346 0.180 1.50e-02 4.44e+03 1.44e+02 bond pdb=" C4' NOS A 501 " pdb=" O4' NOS A 501 " ideal model delta sigma weight residual 1.454 1.309 0.145 1.50e-02 4.44e+03 9.32e+01 bond pdb=" C2 NOS A 501 " pdb=" N3 NOS A 501 " ideal model delta sigma weight residual 1.293 1.444 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" C4 NOS A 501 " pdb=" N3 NOS A 501 " ideal model delta sigma weight residual 1.347 1.497 -0.150 2.00e-02 2.50e+03 5.66e+01 ... (remaining 3993 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 5332 2.00 - 4.00: 75 4.00 - 6.00: 16 6.00 - 8.00: 5 8.00 - 10.00: 1 Bond angle restraints: 5429 Sorted by residual: angle pdb=" C3' NOS A 501 " pdb=" C2' NOS A 501 " pdb=" O2' NOS A 501 " ideal model delta sigma weight residual 114.60 107.68 6.92 1.50e+00 4.44e-01 2.13e+01 angle pdb=" C3' NOS A 501 " pdb=" C4' NOS A 501 " pdb=" C5' NOS A 501 " ideal model delta sigma weight residual 115.20 109.44 5.76 1.50e+00 4.44e-01 1.47e+01 angle pdb=" C1' NOS A 501 " pdb=" O4' NOS A 501 " pdb=" C4' NOS A 501 " ideal model delta sigma weight residual 109.70 106.15 3.55 1.00e+00 1.00e+00 1.26e+01 angle pdb=" C2' NOS A 501 " pdb=" C1' NOS A 501 " pdb=" N9 NOS A 501 " ideal model delta sigma weight residual 114.00 108.75 5.25 1.50e+00 4.44e-01 1.23e+01 angle pdb=" C1' NOS A 501 " pdb=" C2' NOS A 501 " pdb=" C3' NOS A 501 " ideal model delta sigma weight residual 101.50 104.96 -3.46 1.00e+00 1.00e+00 1.20e+01 ... (remaining 5424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.24: 2042 15.24 - 30.48: 191 30.48 - 45.71: 52 45.71 - 60.95: 13 60.95 - 76.19: 3 Dihedral angle restraints: 2301 sinusoidal: 877 harmonic: 1424 Sorted by residual: dihedral pdb=" CA LEU A 256 " pdb=" C LEU A 256 " pdb=" N PHE A 257 " pdb=" CA PHE A 257 " ideal model delta harmonic sigma weight residual -180.00 -161.88 -18.12 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA MET A 145 " pdb=" C MET A 145 " pdb=" N GLU A 146 " pdb=" CA GLU A 146 " ideal model delta harmonic sigma weight residual 180.00 162.85 17.15 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA VAL A 332 " pdb=" C VAL A 332 " pdb=" N ASP A 333 " pdb=" CA ASP A 333 " ideal model delta harmonic sigma weight residual -180.00 -164.41 -15.59 0 5.00e+00 4.00e-02 9.72e+00 ... (remaining 2298 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 372 0.031 - 0.061: 173 0.061 - 0.092: 57 0.092 - 0.122: 20 0.122 - 0.153: 8 Chirality restraints: 630 Sorted by residual: chirality pdb=" CB ILE A 193 " pdb=" CA ILE A 193 " pdb=" CG1 ILE A 193 " pdb=" CG2 ILE A 193 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.82e-01 chirality pdb=" CA ASP A 147 " pdb=" N ASP A 147 " pdb=" C ASP A 147 " pdb=" CB ASP A 147 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" CA PHE A 307 " pdb=" N PHE A 307 " pdb=" C PHE A 307 " pdb=" CB PHE A 307 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.59e-01 ... (remaining 627 not shown) Planarity restraints: 665 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 257 " -0.023 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO A 258 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 258 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 258 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 334 " -0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO A 335 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 335 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 335 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 412 " -0.020 5.00e-02 4.00e+02 3.08e-02 1.51e+00 pdb=" N PRO A 413 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 413 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 413 " -0.017 5.00e-02 4.00e+02 ... (remaining 662 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 835 2.78 - 3.31: 3841 3.31 - 3.84: 6568 3.84 - 4.37: 7875 4.37 - 4.90: 13686 Nonbonded interactions: 32805 Sorted by model distance: nonbonded pdb=" OH TYR A 65 " pdb=" OD1 ASP A 117 " model vdw 2.246 3.040 nonbonded pdb=" OG1 THR A 41 " pdb=" OD1 ASN A 209 " model vdw 2.256 3.040 nonbonded pdb=" O CYS A 395 " pdb=" OG1 THR A 399 " model vdw 2.283 3.040 nonbonded pdb=" O LEU A 256 " pdb=" N GLY A 261 " model vdw 2.320 3.120 nonbonded pdb=" NE2 GLN C 81 " pdb=" OD1 ASN C 83 " model vdw 2.320 3.120 ... (remaining 32800 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: 2.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.730 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 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 : 0.007 0.185 3999 Z= 0.424 Angle : 0.647 10.003 5431 Z= 0.352 Chirality : 0.042 0.153 630 Planarity : 0.004 0.035 665 Dihedral : 13.490 76.187 1384 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 are not related in a simple way. whole: 1.00 (0.38), residues: 487 helix: 1.09 (0.30), residues: 285 sheet: 0.84 (0.64), residues: 58 loop : -0.10 (0.58), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 319 TYR 0.018 0.001 TYR C 102 PHE 0.016 0.001 PHE C 27 TRP 0.009 0.001 TRP A 251 HIS 0.004 0.001 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00728 / 0.42 ( 3998) covalent geometry : angle 0.64751 / 0.35 ( 5429) SS BOND : bond 0.00151 / 0.08 ( 1) SS BOND : angle 0.17564 / 0.09 ( 2) hydrogen bonds : bond 0.18087 / 12.48 ( 256) hydrogen bonds : angle 6.16735 / 4.57 ( 750) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.121 Fit side-chains REVERT: A 175 VAL cc_start: 0.8097 (t) cc_final: 0.7828 (m) REVERT: A 303 LYS cc_start: 0.8628 (tppt) cc_final: 0.8418 (tppt) REVERT: A 407 ASN cc_start: 0.8197 (t0) cc_final: 0.7963 (t0) REVERT: C 94 TYR cc_start: 0.8213 (m-10) cc_final: 0.8003 (m-10) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.0561 time to fit residues: 5.1992 Evaluate side-chains 62 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: [24, 48, 26, 2, 16, 32, 31, 25, 19, 30, 22] chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 135 GLN A 209 ASN C 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.112916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.099657 restraints weight = 5219.303| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.62 r_work: 0.3048 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3999 Z= 0.160 Angle : 0.575 6.512 5431 Z= 0.311 Chirality : 0.043 0.142 630 Planarity : 0.004 0.034 665 Dihedral : 4.635 23.151 518 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.33 % Allowed : 5.35 % Favored : 92.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.38), residues: 487 helix: 1.47 (0.29), residues: 289 sheet: 0.95 (0.64), residues: 58 loop : -0.17 (0.57), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 319 TYR 0.016 0.001 TYR C 102 PHE 0.017 0.001 PHE C 27 TRP 0.012 0.001 TRP A 251 HIS 0.004 0.001 HIS A 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 ( 3998) covalent geometry : angle 0.57462 / 0.31 ( 5429) SS BOND : bond 0.00099 / 0.05 ( 1) SS BOND : angle 0.30428 / 0.16 ( 2) hydrogen bonds : bond 0.05667 / 3.85 ( 256) hydrogen bonds : angle 4.65271 / 3.47 ( 750) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.120 Fit side-chains REVERT: A 303 LYS cc_start: 0.8779 (tppt) cc_final: 0.8564 (tppt) REVERT: A 407 ASN cc_start: 0.8469 (t0) cc_final: 0.8112 (t0) outliers start: 10 outliers final: 5 residues processed: 67 average time/residue: 0.0577 time to fit residues: 4.9295 Evaluate side-chains 61 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain C residue 82 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: [5, 21, 48, 28, 12, 15, 23, 42, 36, 29, 16] chunk 5 optimal weight: 0.0270 chunk 21 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.112962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.099362 restraints weight = 5090.335| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.64 r_work: 0.3067 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3999 Z= 0.136 Angle : 0.533 6.540 5431 Z= 0.287 Chirality : 0.042 0.146 630 Planarity : 0.004 0.034 665 Dihedral : 4.463 24.754 518 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.33 % Allowed : 9.53 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.38), residues: 487 helix: 1.75 (0.29), residues: 288 sheet: 1.10 (0.64), residues: 58 loop : -0.03 (0.59), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 319 TYR 0.018 0.001 TYR C 102 PHE 0.016 0.001 PHE C 27 TRP 0.013 0.001 TRP A 251 HIS 0.002 0.001 HIS A 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 ( 3998) covalent geometry : angle 0.53287 / 0.29 ( 5429) SS BOND : bond 0.00085 / 0.04 ( 1) SS BOND : angle 0.31791 / 0.17 ( 2) hydrogen bonds : bond 0.04994 / 3.40 ( 256) hydrogen bonds : angle 4.36840 / 3.24 ( 750) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.110 Fit side-chains revert: symmetry clash REVERT: A 303 LYS cc_start: 0.8777 (tppt) cc_final: 0.8554 (tppt) outliers start: 10 outliers final: 7 residues processed: 63 average time/residue: 0.0528 time to fit residues: 4.3636 Evaluate side-chains 64 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 82 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: [45, 6, 3, 5, 14, 22, 38, 46, 34, 25, 17] chunk 45 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 0.0870 chunk 14 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 46 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 17 optimal weight: 0.0000 overall best weight: 0.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.115407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.102266 restraints weight = 5117.016| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.58 r_work: 0.3094 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3999 Z= 0.119 Angle : 0.512 7.004 5431 Z= 0.273 Chirality : 0.041 0.148 630 Planarity : 0.004 0.034 665 Dihedral : 4.350 26.394 518 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.02 % Allowed : 11.86 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.38), residues: 487 helix: 1.98 (0.29), residues: 288 sheet: 1.20 (0.64), residues: 58 loop : 0.05 (0.59), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 66 TYR 0.014 0.001 TYR C 102 PHE 0.014 0.001 PHE C 27 TRP 0.013 0.001 TRP A 251 HIS 0.002 0.001 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 ( 3998) covalent geometry : angle 0.51192 / 0.27 ( 5429) SS BOND : bond 0.00052 / 0.03 ( 1) SS BOND : angle 0.24859 / 0.14 ( 2) hydrogen bonds : bond 0.04431 / 3.03 ( 256) hydrogen bonds : angle 4.19909 / 3.10 ( 750) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.142 Fit side-chains revert: symmetry clash REVERT: A 113 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.8237 (m-30) REVERT: A 303 LYS cc_start: 0.8774 (tppt) cc_final: 0.8535 (tppt) outliers start: 13 outliers final: 7 residues processed: 64 average time/residue: 0.0525 time to fit residues: 4.4718 Evaluate side-chains 63 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 88 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: [0, 27, 43, 37, 13, 31, 5, 36, 6, 17, 39] chunk 0 optimal weight: 6.9990 chunk 27 optimal weight: 0.1980 chunk 43 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 5 optimal weight: 0.0370 chunk 36 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 250 ASN A 358 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.115107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.101436 restraints weight = 5128.162| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.63 r_work: 0.3091 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3999 Z= 0.125 Angle : 0.512 6.425 5431 Z= 0.273 Chirality : 0.041 0.153 630 Planarity : 0.004 0.035 665 Dihedral : 4.286 26.700 518 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.72 % Allowed : 12.33 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.38), residues: 487 helix: 1.94 (0.29), residues: 294 sheet: 1.18 (0.65), residues: 58 loop : 0.10 (0.60), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 66 TYR 0.015 0.001 TYR C 102 PHE 0.014 0.001 PHE C 27 TRP 0.011 0.001 TRP A 251 HIS 0.002 0.001 HIS A 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 ( 3998) covalent geometry : angle 0.51250 / 0.27 ( 5429) SS BOND : bond 0.00135 / 0.07 ( 1) SS BOND : angle 0.39296 / 0.21 ( 2) hydrogen bonds : bond 0.04486 / 3.08 ( 256) hydrogen bonds : angle 4.11666 / 3.03 ( 750) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.135 Fit side-chains revert: symmetry clash REVERT: A 113 ASP cc_start: 0.8528 (OUTLIER) cc_final: 0.8290 (m-30) outliers start: 16 outliers final: 10 residues processed: 64 average time/residue: 0.0564 time to fit residues: 4.6351 Evaluate side-chains 64 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 88 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: [18, 30, 46, 13, 0, 36, 17, 25, 34, 41, 27] chunk 18 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.110348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.096553 restraints weight = 5179.023| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.65 r_work: 0.3028 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3999 Z= 0.167 Angle : 0.550 6.821 5431 Z= 0.293 Chirality : 0.043 0.158 630 Planarity : 0.004 0.036 665 Dihedral : 4.387 25.940 518 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.49 % Allowed : 13.26 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.37), residues: 487 helix: 1.81 (0.29), residues: 295 sheet: 1.15 (0.64), residues: 59 loop : -0.14 (0.56), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 291 TYR 0.019 0.001 TYR C 102 PHE 0.015 0.001 PHE C 27 TRP 0.007 0.001 TRP A 251 HIS 0.002 0.001 HIS A 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 ( 3998) covalent geometry : angle 0.55041 / 0.29 ( 5429) SS BOND : bond 0.00145 / 0.08 ( 1) SS BOND : angle 0.47987 / 0.25 ( 2) hydrogen bonds : bond 0.05001 / 3.42 ( 256) hydrogen bonds : angle 4.18538 / 3.08 ( 750) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.140 Fit side-chains REVERT: A 113 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.8307 (m-30) REVERT: C 64 LYS cc_start: 0.7876 (tppp) cc_final: 0.7662 (tppt) outliers start: 15 outliers final: 10 residues processed: 61 average time/residue: 0.0598 time to fit residues: 4.7004 Evaluate side-chains 64 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 88 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: [40, 25, 20, 12, 29, 9, 5, 47, 34, 13, 14] chunk 40 optimal weight: 2.9990 chunk 25 optimal weight: 0.0370 chunk 20 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 0.4980 chunk 9 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.113295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.099392 restraints weight = 5201.142| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.67 r_work: 0.3074 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3999 Z= 0.126 Angle : 0.513 6.631 5431 Z= 0.274 Chirality : 0.041 0.162 630 Planarity : 0.004 0.035 665 Dihedral : 4.311 26.627 518 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.49 % Allowed : 13.72 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.38), residues: 487 helix: 1.97 (0.29), residues: 293 sheet: 1.22 (0.66), residues: 58 loop : 0.13 (0.60), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 66 TYR 0.016 0.001 TYR C 102 PHE 0.012 0.001 PHE C 27 TRP 0.010 0.001 TRP A 251 HIS 0.002 0.001 HIS A 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 ( 3998) covalent geometry : angle 0.51313 / 0.27 ( 5429) SS BOND : bond 0.00092 / 0.05 ( 1) SS BOND : angle 0.41346 / 0.22 ( 2) hydrogen bonds : bond 0.04490 / 3.07 ( 256) hydrogen bonds : angle 4.09211 / 3.01 ( 750) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.132 Fit side-chains REVERT: A 113 ASP cc_start: 0.8485 (OUTLIER) cc_final: 0.8243 (m-30) outliers start: 15 outliers final: 10 residues processed: 65 average time/residue: 0.0531 time to fit residues: 4.5336 Evaluate side-chains 64 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 88 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: [35, 30, 13, 15, 39, 40, 4, 14, 45, 6, 10] chunk 35 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.110231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.096394 restraints weight = 5143.714| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.65 r_work: 0.3028 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3999 Z= 0.169 Angle : 0.546 6.249 5431 Z= 0.294 Chirality : 0.043 0.162 630 Planarity : 0.004 0.036 665 Dihedral : 4.393 26.587 518 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.26 % Allowed : 15.12 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.37), residues: 487 helix: 1.80 (0.29), residues: 295 sheet: 1.09 (0.65), residues: 59 loop : -0.10 (0.57), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 291 TYR 0.018 0.001 TYR C 102 PHE 0.014 0.001 PHE C 27 TRP 0.007 0.001 TRP A 251 HIS 0.002 0.001 HIS A 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 ( 3998) covalent geometry : angle 0.54601 / 0.29 ( 5429) SS BOND : bond 0.00181 / 0.10 ( 1) SS BOND : angle 0.48436 / 0.26 ( 2) hydrogen bonds : bond 0.05018 / 3.43 ( 256) hydrogen bonds : angle 4.15752 / 3.05 ( 750) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.109 Fit side-chains REVERT: A 113 ASP cc_start: 0.8520 (OUTLIER) cc_final: 0.8304 (m-30) REVERT: C 64 LYS cc_start: 0.7537 (tppt) cc_final: 0.7186 (mttp) outliers start: 14 outliers final: 12 residues processed: 65 average time/residue: 0.0596 time to fit residues: 4.9511 Evaluate side-chains 69 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 88 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: [26, 23, 36, 44, 13, 7, 47, 17, 28, 21, 10] chunk 26 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.111857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.097903 restraints weight = 5161.766| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.67 r_work: 0.3048 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3999 Z= 0.144 Angle : 0.533 7.012 5431 Z= 0.286 Chirality : 0.042 0.168 630 Planarity : 0.004 0.035 665 Dihedral : 4.361 26.382 518 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.79 % Allowed : 15.35 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.38), residues: 487 helix: 1.90 (0.29), residues: 294 sheet: 1.13 (0.65), residues: 59 loop : 0.05 (0.59), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 66 TYR 0.018 0.001 TYR C 102 PHE 0.013 0.001 PHE C 27 TRP 0.008 0.001 TRP A 251 HIS 0.002 0.001 HIS A 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 3998) covalent geometry : angle 0.53310 / 0.29 ( 5429) SS BOND : bond 0.00124 / 0.07 ( 1) SS BOND : angle 0.41739 / 0.22 ( 2) hydrogen bonds : bond 0.04722 / 3.23 ( 256) hydrogen bonds : angle 4.11304 / 3.01 ( 750) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.144 Fit side-chains REVERT: A 113 ASP cc_start: 0.8479 (OUTLIER) cc_final: 0.8259 (m-30) REVERT: A 375 LYS cc_start: 0.8494 (ttmm) cc_final: 0.8140 (mmtt) REVERT: C 64 LYS cc_start: 0.7553 (tppt) cc_final: 0.7210 (mttp) outliers start: 12 outliers final: 10 residues processed: 61 average time/residue: 0.0624 time to fit residues: 4.8510 Evaluate side-chains 65 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 88 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: [20, 13, 38, 29, 0, 48, 6, 25, 7, 16, 3] chunk 20 optimal weight: 0.1980 chunk 13 optimal weight: 0.9980 chunk 38 optimal weight: 0.0980 chunk 29 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 48 optimal weight: 0.0980 chunk 6 optimal weight: 0.9990 chunk 25 optimal weight: 0.1980 chunk 7 optimal weight: 0.9990 chunk 16 optimal weight: 0.2980 chunk 3 optimal weight: 0.7980 overall best weight: 0.1780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.118344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.104455 restraints weight = 5124.488| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.68 r_work: 0.3149 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3999 Z= 0.109 Angle : 0.505 8.204 5431 Z= 0.267 Chirality : 0.041 0.174 630 Planarity : 0.004 0.034 665 Dihedral : 4.219 29.789 518 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.56 % Allowed : 15.81 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.39), residues: 487 helix: 2.20 (0.29), residues: 293 sheet: 1.31 (0.66), residues: 58 loop : 0.27 (0.61), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 66 TYR 0.012 0.001 TYR C 102 PHE 0.012 0.001 PHE C 27 TRP 0.017 0.001 TRP A 251 HIS 0.002 0.000 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.11 ( 3998) covalent geometry : angle 0.50470 / 0.27 ( 5429) SS BOND : bond 0.00011 / 0.01 ( 1) SS BOND : angle 0.43991 / 0.26 ( 2) hydrogen bonds : bond 0.03927 / 2.71 ( 256) hydrogen bonds : angle 3.94194 / 2.88 ( 750) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.082 Fit side-chains REVERT: A 113 ASP cc_start: 0.8462 (OUTLIER) cc_final: 0.8204 (m-30) REVERT: A 303 LYS cc_start: 0.8747 (tppt) cc_final: 0.8134 (pttt) REVERT: C 64 LYS cc_start: 0.7405 (tppt) cc_final: 0.7137 (mttp) outliers start: 11 outliers final: 8 residues processed: 66 average time/residue: 0.0509 time to fit residues: 4.4538 Evaluate side-chains 62 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 82 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: [14, 25, 7, 23, 16, 30, 40, 48, 18, 29, 46] chunk 14 optimal weight: 0.0000 chunk 25 optimal weight: 0.1980 chunk 7 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 29 optimal weight: 0.2980 chunk 46 optimal weight: 0.6980 overall best weight: 0.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.117460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.103366 restraints weight = 5132.642| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.70 r_work: 0.3130 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3999 Z= 0.116 Angle : 0.512 7.849 5431 Z= 0.271 Chirality : 0.041 0.168 630 Planarity : 0.004 0.035 665 Dihedral : 4.186 29.508 518 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.79 % Allowed : 16.51 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.36 (0.39), residues: 487 helix: 2.21 (0.29), residues: 291 sheet: 1.26 (0.67), residues: 58 loop : 0.39 (0.61), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 66 TYR 0.013 0.001 TYR A 119 PHE 0.012 0.001 PHE C 27 TRP 0.013 0.001 TRP A 251 HIS 0.002 0.001 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 ( 3998) covalent geometry : angle 0.51209 / 0.27 ( 5429) SS BOND : bond 0.00060 / 0.03 ( 1) SS BOND : angle 0.40968 / 0.23 ( 2) hydrogen bonds : bond 0.04074 / 2.81 ( 256) hydrogen bonds : angle 3.95688 / 2.90 ( 750) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1068.27 seconds wall clock time: 19 minutes 5.91 seconds (1145.91 seconds total)