Starting phenix.real_space_refine on Wed Sep 17 03:17:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kqe_62501/09_2025/9kqe_62501.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kqe_62501/09_2025/9kqe_62501.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kqe_62501/09_2025/9kqe_62501.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kqe_62501/09_2025/9kqe_62501.map" model { file = "/net/cci-nas-00/data/ceres_data/9kqe_62501/09_2025/9kqe_62501.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kqe_62501/09_2025/9kqe_62501.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.075 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 1863 2.51 5 N 433 2.21 5 O 471 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2795 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2784 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 23, 'TRANS': 349} Chain breaks: 1 Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'LDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.97, per 1000 atoms: 0.35 Number of scatterers: 2795 At special positions: 0 Unit cell: (68.036, 54.056, 62.444, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 471 8.00 N 433 7.00 C 1863 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.30 Conformation dependent library (CDL) restraints added in 136.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 670 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 0 sheets defined 91.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 18 through 44 removed outlier: 3.916A pdb=" N ILE A 22 " --> pdb=" O SER A 18 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Proline residue: A 42 - end of helix Processing helix chain 'A' and resid 133 through 157 removed outlier: 4.443A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ALA A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 4.132A pdb=" N ASN A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 178 removed outlier: 3.889A pdb=" N GLY A 165 " --> pdb=" O PRO A 161 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N PHE A 166 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N CYS A 167 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET A 169 " --> pdb=" O GLY A 165 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A 178 " --> pdb=" O ILE A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 211 Processing helix chain 'A' and resid 213 through 234 removed outlier: 3.780A pdb=" N ASN A 219 " --> pdb=" O GLU A 215 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 246 removed outlier: 3.708A pdb=" N PHE A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 270 Processing helix chain 'A' and resid 284 through 290 Processing helix chain 'A' and resid 291 through 323 Proline residue: A 313 - end of helix Proline residue: A 316 - end of helix removed outlier: 4.068A pdb=" N GLU A 321 " --> pdb=" O ILE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 333 Processing helix chain 'A' and resid 334 through 356 removed outlier: 3.798A pdb=" N SER A 338 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ILE A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N HIS A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 374 Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 385 through 413 removed outlier: 3.991A pdb=" N SER A 401 " --> pdb=" O MET A 397 " (cutoff:3.500A) Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 418 through 448 removed outlier: 3.972A pdb=" N GLY A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR A 433 " --> pdb=" O PHE A 429 " (cutoff:3.500A) Proline residue: A 437 - end of helix Processing helix chain 'A' and resid 448 through 464 Processing helix chain 'A' and resid 465 through 471 233 hydrogen bonds defined for protein. 681 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.41 Time building geometry restraints manager: 0.35 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: 558 1.33 - 1.45: 618 1.45 - 1.57: 1638 1.57 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 2862 Sorted by residual: bond pdb=" CA SER A 197 " pdb=" C SER A 197 " ideal model delta sigma weight residual 1.524 1.487 0.037 1.27e-02 6.20e+03 8.31e+00 bond pdb=" CA SER A 209 " pdb=" C SER A 209 " ideal model delta sigma weight residual 1.523 1.489 0.033 1.37e-02 5.33e+03 5.97e+00 bond pdb=" C ILE A 301 " pdb=" O ILE A 301 " ideal model delta sigma weight residual 1.237 1.209 0.028 1.17e-02 7.31e+03 5.74e+00 bond pdb=" CA LYS A 281 " pdb=" C LYS A 281 " ideal model delta sigma weight residual 1.524 1.493 0.031 1.35e-02 5.49e+03 5.22e+00 bond pdb=" CA ASP A 291 " pdb=" C ASP A 291 " ideal model delta sigma weight residual 1.524 1.502 0.022 1.08e-02 8.57e+03 4.07e+00 ... (remaining 2857 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 3619 1.42 - 2.84: 203 2.84 - 4.25: 42 4.25 - 5.67: 21 5.67 - 7.09: 6 Bond angle restraints: 3891 Sorted by residual: angle pdb=" CA ILE A 44 " pdb=" C ILE A 44 " pdb=" N PRO A 45 " ideal model delta sigma weight residual 120.83 117.47 3.36 5.90e-01 2.87e+00 3.24e+01 angle pdb=" C ILE A 44 " pdb=" CA ILE A 44 " pdb=" CB ILE A 44 " ideal model delta sigma weight residual 113.70 108.57 5.13 9.50e-01 1.11e+00 2.92e+01 angle pdb=" N VAL A 427 " pdb=" CA VAL A 427 " pdb=" C VAL A 427 " ideal model delta sigma weight residual 111.00 106.05 4.95 1.09e+00 8.42e-01 2.06e+01 angle pdb=" N ARG A 274 " pdb=" CA ARG A 274 " pdb=" C ARG A 274 " ideal model delta sigma weight residual 109.95 116.90 -6.95 1.59e+00 3.96e-01 1.91e+01 angle pdb=" N VAL A 417 " pdb=" CA VAL A 417 " pdb=" C VAL A 417 " ideal model delta sigma weight residual 108.12 102.17 5.95 1.44e+00 4.82e-01 1.71e+01 ... (remaining 3886 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.77: 1442 12.77 - 25.53: 156 25.53 - 38.30: 53 38.30 - 51.07: 19 51.07 - 63.83: 6 Dihedral angle restraints: 1676 sinusoidal: 624 harmonic: 1052 Sorted by residual: dihedral pdb=" CA TYR A 422 " pdb=" C TYR A 422 " pdb=" N ALA A 423 " pdb=" CA ALA A 423 " ideal model delta harmonic sigma weight residual 180.00 163.34 16.66 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA ASN A 146 " pdb=" CB ASN A 146 " pdb=" CG ASN A 146 " pdb=" OD1 ASN A 146 " ideal model delta sinusoidal sigma weight residual 120.00 -176.17 -63.83 2 2.00e+01 2.50e-03 9.67e+00 dihedral pdb=" CA ASP A 213 " pdb=" CB ASP A 213 " pdb=" CG ASP A 213 " pdb=" OD1 ASP A 213 " ideal model delta sinusoidal sigma weight residual -30.00 -82.90 52.90 1 2.00e+01 2.50e-03 9.52e+00 ... (remaining 1673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 255 0.030 - 0.061: 133 0.061 - 0.091: 47 0.091 - 0.121: 23 0.121 - 0.152: 7 Chirality restraints: 465 Sorted by residual: chirality pdb=" CA PHE A 348 " pdb=" N PHE A 348 " pdb=" C PHE A 348 " pdb=" CB PHE A 348 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.76e-01 chirality pdb=" CA PRO A 159 " pdb=" N PRO A 159 " pdb=" C PRO A 159 " pdb=" CB PRO A 159 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.97e-01 chirality pdb=" CA SER A 199 " pdb=" N SER A 199 " pdb=" C SER A 199 " pdb=" CB SER A 199 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.54e-01 ... (remaining 462 not shown) Planarity restraints: 476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 164 " 0.009 2.00e-02 2.50e+03 1.77e-02 3.15e+00 pdb=" C ALA A 164 " -0.031 2.00e-02 2.50e+03 pdb=" O ALA A 164 " 0.011 2.00e-02 2.50e+03 pdb=" N GLY A 165 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 235 " -0.025 5.00e-02 4.00e+02 3.73e-02 2.23e+00 pdb=" N PRO A 236 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 236 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 236 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 404 " -0.007 2.00e-02 2.50e+03 1.44e-02 2.07e+00 pdb=" C PRO A 404 " 0.025 2.00e-02 2.50e+03 pdb=" O PRO A 404 " -0.009 2.00e-02 2.50e+03 pdb=" N ILE A 405 " -0.008 2.00e-02 2.50e+03 ... (remaining 473 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 637 2.77 - 3.30: 2790 3.30 - 3.83: 4758 3.83 - 4.37: 5520 4.37 - 4.90: 9703 Nonbonded interactions: 23408 Sorted by model distance: nonbonded pdb=" O ILE A 301 " pdb=" ND2 ASN A 305 " model vdw 2.237 3.120 nonbonded pdb=" O THR A 212 " pdb=" OG1 THR A 212 " model vdw 2.324 3.040 nonbonded pdb=" O PRO A 336 " pdb=" OG SER A 340 " model vdw 2.417 3.040 nonbonded pdb=" NH2 ARG A 19 " pdb=" OE1 GLU A 216 " model vdw 2.466 3.120 nonbonded pdb=" OE1 GLU A 215 " pdb=" ND1 HIS A 353 " model vdw 2.481 3.120 ... (remaining 23403 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.090 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:6.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 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 : 0.008 0.059 2862 Z= 0.381 Angle : 0.868 7.088 3891 Z= 0.532 Chirality : 0.046 0.152 465 Planarity : 0.005 0.037 476 Dihedral : 13.458 63.834 1006 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.68 % Allowed : 14.09 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.23 (0.39), residues: 369 helix: -1.07 (0.27), residues: 297 sheet: None (None), residues: 0 loop : -2.52 (0.61), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 413 TYR 0.019 0.002 TYR A 422 PHE 0.014 0.002 PHE A 348 TRP 0.006 0.001 TRP A 318 HIS 0.004 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00761 ( 2862) covalent geometry : angle 0.86831 ( 3891) hydrogen bonds : bond 0.15010 ( 233) hydrogen bonds : angle 7.30495 ( 681) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 0.107 Fit side-chains REVERT: A 322 THR cc_start: 0.8357 (m) cc_final: 0.8087 (p) REVERT: A 397 MET cc_start: 0.8037 (ttt) cc_final: 0.7697 (ttm) outliers start: 5 outliers final: 3 residues processed: 100 average time/residue: 0.2894 time to fit residues: 30.1616 Evaluate side-chains 72 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.174297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.155598 restraints weight = 3447.837| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.24 r_work: 0.3748 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2862 Z= 0.171 Angle : 0.680 6.745 3891 Z= 0.342 Chirality : 0.044 0.128 465 Planarity : 0.005 0.035 476 Dihedral : 5.946 52.533 398 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 5.70 % Allowed : 22.15 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.43), residues: 369 helix: 0.42 (0.29), residues: 312 sheet: None (None), residues: 0 loop : -2.06 (0.70), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 357 TYR 0.015 0.002 TYR A 422 PHE 0.020 0.002 PHE A 468 TRP 0.008 0.001 TRP A 451 HIS 0.001 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 2862) covalent geometry : angle 0.68012 ( 3891) hydrogen bonds : bond 0.04772 ( 233) hydrogen bonds : angle 5.09843 ( 681) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.122 Fit side-chains revert: symmetry clash REVERT: A 179 SER cc_start: 0.7261 (OUTLIER) cc_final: 0.6946 (m) REVERT: A 291 ASP cc_start: 0.8814 (t0) cc_final: 0.8545 (t0) REVERT: A 322 THR cc_start: 0.8415 (m) cc_final: 0.7872 (p) REVERT: A 397 MET cc_start: 0.8445 (ttt) cc_final: 0.8197 (ttm) outliers start: 17 outliers final: 8 residues processed: 85 average time/residue: 0.3494 time to fit residues: 30.8904 Evaluate side-chains 77 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 14 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.171575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.152253 restraints weight = 3473.086| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 2.23 r_work: 0.3714 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2862 Z= 0.171 Angle : 0.693 9.085 3891 Z= 0.339 Chirality : 0.043 0.141 465 Planarity : 0.005 0.031 476 Dihedral : 5.516 57.051 396 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 5.70 % Allowed : 26.17 % Favored : 68.12 % 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 aren not related in a simple way. whole: 0.79 (0.44), residues: 369 helix: 1.00 (0.30), residues: 313 sheet: None (None), residues: 0 loop : -1.88 (0.71), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 217 TYR 0.018 0.002 TYR A 422 PHE 0.012 0.001 PHE A 238 TRP 0.006 0.001 TRP A 451 HIS 0.002 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 2862) covalent geometry : angle 0.69265 ( 3891) hydrogen bonds : bond 0.04717 ( 233) hydrogen bonds : angle 4.89024 ( 681) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.103 Fit side-chains revert: symmetry clash REVERT: A 179 SER cc_start: 0.7533 (OUTLIER) cc_final: 0.7042 (m) REVERT: A 278 GLU cc_start: 0.7929 (mp0) cc_final: 0.7725 (mp0) REVERT: A 291 ASP cc_start: 0.8830 (t0) cc_final: 0.8586 (t70) REVERT: A 322 THR cc_start: 0.8501 (m) cc_final: 0.7963 (p) REVERT: A 397 MET cc_start: 0.8496 (ttt) cc_final: 0.8287 (ttm) outliers start: 17 outliers final: 10 residues processed: 77 average time/residue: 0.3453 time to fit residues: 27.6208 Evaluate side-chains 72 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 32 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 35 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: A 34 ASN ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 ASN ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.170858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.151313 restraints weight = 3455.408| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 2.24 r_work: 0.3713 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2862 Z= 0.177 Angle : 0.701 9.127 3891 Z= 0.340 Chirality : 0.044 0.131 465 Planarity : 0.005 0.031 476 Dihedral : 5.342 59.544 394 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 6.38 % Allowed : 27.18 % Favored : 66.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.45), residues: 369 helix: 1.20 (0.31), residues: 313 sheet: None (None), residues: 0 loop : -1.64 (0.71), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 217 TYR 0.016 0.002 TYR A 422 PHE 0.013 0.001 PHE A 238 TRP 0.005 0.001 TRP A 451 HIS 0.002 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 2862) covalent geometry : angle 0.70112 ( 3891) hydrogen bonds : bond 0.04698 ( 233) hydrogen bonds : angle 4.78142 ( 681) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.103 Fit side-chains REVERT: A 179 SER cc_start: 0.7514 (OUTLIER) cc_final: 0.6959 (m) REVERT: A 234 VAL cc_start: 0.8742 (p) cc_final: 0.8431 (m) REVERT: A 291 ASP cc_start: 0.8846 (t0) cc_final: 0.8598 (t70) REVERT: A 322 THR cc_start: 0.8481 (m) cc_final: 0.7844 (p) REVERT: A 397 MET cc_start: 0.8552 (ttt) cc_final: 0.8327 (ttm) outliers start: 19 outliers final: 8 residues processed: 76 average time/residue: 0.3326 time to fit residues: 26.3473 Evaluate side-chains 67 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 472 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 0.0070 chunk 8 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 ASN ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.175888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.156030 restraints weight = 3379.551| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.25 r_work: 0.3751 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2862 Z= 0.161 Angle : 0.683 9.557 3891 Z= 0.333 Chirality : 0.043 0.128 465 Planarity : 0.005 0.029 476 Dihedral : 5.262 58.068 394 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 5.37 % Allowed : 28.86 % Favored : 65.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.46), residues: 369 helix: 1.34 (0.31), residues: 314 sheet: None (None), residues: 0 loop : -1.77 (0.73), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 217 TYR 0.019 0.002 TYR A 422 PHE 0.013 0.001 PHE A 238 TRP 0.005 0.001 TRP A 451 HIS 0.001 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 2862) covalent geometry : angle 0.68299 ( 3891) hydrogen bonds : bond 0.04550 ( 233) hydrogen bonds : angle 4.71379 ( 681) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.107 Fit side-chains REVERT: A 179 SER cc_start: 0.7556 (OUTLIER) cc_final: 0.7056 (m) REVERT: A 291 ASP cc_start: 0.8822 (t0) cc_final: 0.8571 (t70) REVERT: A 388 ASN cc_start: 0.8875 (m110) cc_final: 0.8569 (m110) REVERT: A 397 MET cc_start: 0.8565 (ttt) cc_final: 0.8357 (ttm) outliers start: 16 outliers final: 8 residues processed: 75 average time/residue: 0.3443 time to fit residues: 26.8732 Evaluate side-chains 65 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.169457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.149650 restraints weight = 3458.989| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.26 r_work: 0.3709 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2862 Z= 0.175 Angle : 0.717 11.276 3891 Z= 0.340 Chirality : 0.043 0.130 465 Planarity : 0.005 0.029 476 Dihedral : 5.149 55.672 394 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 6.04 % Allowed : 28.52 % Favored : 65.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.46), residues: 369 helix: 1.41 (0.31), residues: 314 sheet: None (None), residues: 0 loop : -1.85 (0.73), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 217 TYR 0.020 0.002 TYR A 422 PHE 0.013 0.001 PHE A 238 TRP 0.004 0.001 TRP A 451 HIS 0.002 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 2862) covalent geometry : angle 0.71680 ( 3891) hydrogen bonds : bond 0.04653 ( 233) hydrogen bonds : angle 4.72109 ( 681) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.123 Fit side-chains REVERT: A 179 SER cc_start: 0.7473 (OUTLIER) cc_final: 0.7062 (m) REVERT: A 230 MET cc_start: 0.7580 (tmt) cc_final: 0.7336 (tmt) REVERT: A 234 VAL cc_start: 0.8675 (p) cc_final: 0.8466 (m) REVERT: A 291 ASP cc_start: 0.8862 (t0) cc_final: 0.8621 (t70) REVERT: A 317 ILE cc_start: 0.8676 (mm) cc_final: 0.8404 (mt) REVERT: A 388 ASN cc_start: 0.8933 (m110) cc_final: 0.8574 (m110) REVERT: A 397 MET cc_start: 0.8594 (ttt) cc_final: 0.8355 (ttm) REVERT: A 417 VAL cc_start: 0.8394 (t) cc_final: 0.7997 (m) outliers start: 18 outliers final: 9 residues processed: 74 average time/residue: 0.3715 time to fit residues: 28.5615 Evaluate side-chains 68 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 24 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 21 optimal weight: 0.0470 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.171273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.152229 restraints weight = 3460.111| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 2.13 r_work: 0.3745 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2862 Z= 0.153 Angle : 0.702 11.534 3891 Z= 0.332 Chirality : 0.042 0.127 465 Planarity : 0.005 0.030 476 Dihedral : 5.017 52.330 394 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 5.37 % Allowed : 29.19 % Favored : 65.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.46), residues: 369 helix: 1.52 (0.31), residues: 314 sheet: None (None), residues: 0 loop : -1.81 (0.73), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 357 TYR 0.014 0.002 TYR A 422 PHE 0.013 0.001 PHE A 166 TRP 0.006 0.001 TRP A 318 HIS 0.001 0.000 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 2862) covalent geometry : angle 0.70157 ( 3891) hydrogen bonds : bond 0.04388 ( 233) hydrogen bonds : angle 4.61512 ( 681) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.111 Fit side-chains REVERT: A 35 MET cc_start: 0.8537 (ttm) cc_final: 0.8219 (ttt) REVERT: A 179 SER cc_start: 0.7440 (OUTLIER) cc_final: 0.7171 (m) REVERT: A 291 ASP cc_start: 0.8832 (t0) cc_final: 0.8581 (t70) REVERT: A 317 ILE cc_start: 0.8732 (mm) cc_final: 0.8490 (mt) REVERT: A 319 MET cc_start: 0.8406 (ttm) cc_final: 0.8192 (mtp) REVERT: A 388 ASN cc_start: 0.8900 (m110) cc_final: 0.8574 (m110) REVERT: A 417 VAL cc_start: 0.8392 (t) cc_final: 0.7992 (m) outliers start: 16 outliers final: 8 residues processed: 77 average time/residue: 0.3306 time to fit residues: 26.5317 Evaluate side-chains 65 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 472 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 11 optimal weight: 0.0970 chunk 30 optimal weight: 0.2980 chunk 6 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 33 optimal weight: 0.3980 chunk 23 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.172952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.153102 restraints weight = 3513.403| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.32 r_work: 0.3736 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2862 Z= 0.148 Angle : 0.713 12.245 3891 Z= 0.333 Chirality : 0.043 0.157 465 Planarity : 0.004 0.030 476 Dihedral : 4.911 49.434 394 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.36 % Allowed : 32.89 % Favored : 63.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.46), residues: 369 helix: 1.56 (0.31), residues: 315 sheet: None (None), residues: 0 loop : -1.92 (0.72), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 357 TYR 0.015 0.002 TYR A 422 PHE 0.013 0.001 PHE A 348 TRP 0.004 0.001 TRP A 318 HIS 0.001 0.000 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 2862) covalent geometry : angle 0.71260 ( 3891) hydrogen bonds : bond 0.04299 ( 233) hydrogen bonds : angle 4.55461 ( 681) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.082 Fit side-chains REVERT: A 160 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8440 (mp) REVERT: A 291 ASP cc_start: 0.8902 (t0) cc_final: 0.8620 (t70) REVERT: A 320 MET cc_start: 0.8897 (mtp) cc_final: 0.8559 (mtp) outliers start: 10 outliers final: 6 residues processed: 72 average time/residue: 0.3315 time to fit residues: 24.8671 Evaluate side-chains 64 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 472 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 2 optimal weight: 0.0970 chunk 0 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 0.3980 chunk 17 optimal weight: 0.0980 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 4 optimal weight: 0.0980 chunk 27 optimal weight: 0.0770 chunk 33 optimal weight: 0.6980 overall best weight: 0.1536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 ASN ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.177385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.158414 restraints weight = 3506.790| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 2.18 r_work: 0.3815 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2862 Z= 0.134 Angle : 0.706 11.457 3891 Z= 0.329 Chirality : 0.042 0.129 465 Planarity : 0.005 0.034 476 Dihedral : 4.817 47.440 394 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.35 % Allowed : 35.23 % Favored : 62.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.46), residues: 369 helix: 1.69 (0.31), residues: 310 sheet: None (None), residues: 0 loop : -1.47 (0.74), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 326 TYR 0.012 0.001 TYR A 422 PHE 0.013 0.001 PHE A 348 TRP 0.002 0.001 TRP A 358 HIS 0.000 0.000 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 2862) covalent geometry : angle 0.70639 ( 3891) hydrogen bonds : bond 0.03993 ( 233) hydrogen bonds : angle 4.51406 ( 681) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.061 Fit side-chains REVERT: A 35 MET cc_start: 0.8477 (ttm) cc_final: 0.8050 (ttt) REVERT: A 291 ASP cc_start: 0.8843 (t0) cc_final: 0.8584 (t70) outliers start: 7 outliers final: 6 residues processed: 73 average time/residue: 0.3164 time to fit residues: 24.0317 Evaluate side-chains 67 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 472 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 12 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 17 optimal weight: 0.0060 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.179865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.159602 restraints weight = 3431.362| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 2.31 r_work: 0.3773 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2862 Z= 0.163 Angle : 0.765 11.891 3891 Z= 0.352 Chirality : 0.044 0.140 465 Planarity : 0.005 0.033 476 Dihedral : 4.859 46.854 394 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.68 % Allowed : 36.24 % Favored : 61.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.46), residues: 369 helix: 1.71 (0.31), residues: 310 sheet: None (None), residues: 0 loop : -1.54 (0.74), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 155 TYR 0.018 0.002 TYR A 422 PHE 0.012 0.001 PHE A 348 TRP 0.004 0.001 TRP A 451 HIS 0.001 0.000 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 2862) covalent geometry : angle 0.76547 ( 3891) hydrogen bonds : bond 0.04309 ( 233) hydrogen bonds : angle 4.53575 ( 681) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.103 Fit side-chains REVERT: A 35 MET cc_start: 0.8521 (ttm) cc_final: 0.8017 (ttt) REVERT: A 291 ASP cc_start: 0.8914 (t0) cc_final: 0.8628 (t70) outliers start: 8 outliers final: 4 residues processed: 68 average time/residue: 0.3425 time to fit residues: 24.1664 Evaluate side-chains 66 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 472 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 17 optimal weight: 0.0980 chunk 15 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 34 optimal weight: 0.0670 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.177617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.157257 restraints weight = 3363.389| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 2.27 r_work: 0.3758 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2862 Z= 0.155 Angle : 0.755 11.804 3891 Z= 0.351 Chirality : 0.044 0.131 465 Planarity : 0.005 0.034 476 Dihedral : 4.822 46.275 394 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.68 % Allowed : 37.25 % Favored : 61.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.46), residues: 369 helix: 1.66 (0.31), residues: 310 sheet: None (None), residues: 0 loop : -1.46 (0.75), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 357 TYR 0.017 0.002 TYR A 422 PHE 0.015 0.001 PHE A 166 TRP 0.003 0.001 TRP A 451 HIS 0.002 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 2862) covalent geometry : angle 0.75546 ( 3891) hydrogen bonds : bond 0.04274 ( 233) hydrogen bonds : angle 4.55262 ( 681) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1022.19 seconds wall clock time: 18 minutes 12.20 seconds (1092.20 seconds total)