Starting phenix.real_space_refine on Fri Aug 22 16:16:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iew_35374/08_2025/8iew_35374.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iew_35374/08_2025/8iew_35374.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iew_35374/08_2025/8iew_35374.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iew_35374/08_2025/8iew_35374.map" model { file = "/net/cci-nas-00/data/ceres_data/8iew_35374/08_2025/8iew_35374.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iew_35374/08_2025/8iew_35374.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 546 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 65 5.49 5 S 8 5.16 5 C 3141 2.51 5 N 969 2.21 5 O 1138 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5321 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3966 Classifications: {'peptide': 498} Link IDs: {'PTRANS': 37, 'TRANS': 460} Chain breaks: 2 Chain: "B" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 753 Classifications: {'RNA': 36} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 8, 'rna3p_pur': 11, 'rna3p_pyr': 16} Link IDs: {'rna2p': 9, 'rna3p': 26} Chain: "C" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 463 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "D" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 139 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Time building chain proxies: 1.61, per 1000 atoms: 0.30 Number of scatterers: 5321 At special positions: 0 Unit cell: (85.8, 90.42, 97.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 8 16.00 P 65 15.00 O 1138 8.00 N 969 7.00 C 3141 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: 0.47 Conformation dependent library (CDL) restraints added in 157.9 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 932 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 2 sheets defined 49.4% alpha, 8.2% beta 19 base pairs and 40 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 75 through 90 removed outlier: 3.571A pdb=" N GLY A 90 " --> pdb=" O GLU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 99 removed outlier: 4.091A pdb=" N GLU A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 116 Processing helix chain 'A' and resid 125 through 141 removed outlier: 6.579A pdb=" N LEU A 131 " --> pdb=" O GLN A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 168 removed outlier: 3.680A pdb=" N LYS A 146 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 163 " --> pdb=" O THR A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.878A pdb=" N ILE A 238 " --> pdb=" O ARG A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 270 Processing helix chain 'A' and resid 281 through 291 removed outlier: 3.910A pdb=" N LEU A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 319 removed outlier: 3.559A pdb=" N ARG A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 334 Processing helix chain 'A' and resid 367 through 380 removed outlier: 4.158A pdb=" N LYS A 371 " --> pdb=" O GLY A 367 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU A 372 " --> pdb=" O LYS A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 450 removed outlier: 3.525A pdb=" N GLU A 441 " --> pdb=" O ASP A 437 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA A 445 " --> pdb=" O GLU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 464 removed outlier: 3.842A pdb=" N GLU A 458 " --> pdb=" O GLU A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 558 Processing helix chain 'A' and resid 558 through 586 removed outlier: 3.851A pdb=" N LYS A 568 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR A 569 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A 584 " --> pdb=" O VAL A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 642 removed outlier: 3.906A pdb=" N LEU A 638 " --> pdb=" O ALA A 634 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ALA A 639 " --> pdb=" O PHE A 635 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU A 640 " --> pdb=" O SER A 636 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 198 through 199 removed outlier: 3.914A pdb=" N ILE A 347 " --> pdb=" O ASP A 342 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN A 64 " --> pdb=" O ASP A 308 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL A 306 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N GLN A 68 " --> pdb=" O TRP A 304 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N TRP A 304 " --> pdb=" O GLN A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 417 through 420 removed outlier: 4.117A pdb=" N GLY A 417 " --> pdb=" O PHE A 401 " (cutoff:3.500A) 185 hydrogen bonds defined for protein. 525 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 48 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 40 stacking parallelities Total time for adding SS restraints: 0.64 Time building geometry restraints manager: 0.62 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: 1351 1.33 - 1.45: 1300 1.45 - 1.57: 2780 1.57 - 1.69: 127 1.69 - 1.81: 11 Bond restraints: 5569 Sorted by residual: bond pdb=" C TYR A 87 " pdb=" N VAL A 88 " ideal model delta sigma weight residual 1.334 1.291 0.043 1.26e-02 6.30e+03 1.16e+01 bond pdb=" C SER A 205 " pdb=" N PRO A 206 " ideal model delta sigma weight residual 1.331 1.359 -0.027 1.20e-02 6.94e+03 5.24e+00 bond pdb=" CA TYR A 87 " pdb=" C TYR A 87 " ideal model delta sigma weight residual 1.524 1.497 0.027 1.32e-02 5.74e+03 4.06e+00 bond pdb=" O5' C B 8 " pdb=" C5' C B 8 " ideal model delta sigma weight residual 1.424 1.452 -0.028 1.50e-02 4.44e+03 3.43e+00 bond pdb=" P C B 8 " pdb=" OP2 C B 8 " ideal model delta sigma weight residual 1.485 1.519 -0.034 2.00e-02 2.50e+03 2.86e+00 ... (remaining 5564 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 7727 2.35 - 4.71: 90 4.71 - 7.06: 13 7.06 - 9.41: 2 9.41 - 11.76: 1 Bond angle restraints: 7833 Sorted by residual: angle pdb=" O GLU A 86 " pdb=" C GLU A 86 " pdb=" N TYR A 87 " ideal model delta sigma weight residual 122.12 117.45 4.67 1.06e+00 8.90e-01 1.94e+01 angle pdb=" C TYR A 87 " pdb=" N VAL A 88 " pdb=" CA VAL A 88 " ideal model delta sigma weight residual 120.42 114.47 5.95 1.42e+00 4.96e-01 1.76e+01 angle pdb=" CA PRO A 247 " pdb=" N PRO A 247 " pdb=" CD PRO A 247 " ideal model delta sigma weight residual 112.00 106.30 5.70 1.40e+00 5.10e-01 1.66e+01 angle pdb=" CA GLU A 86 " pdb=" C GLU A 86 " pdb=" N TYR A 87 " ideal model delta sigma weight residual 117.30 121.91 -4.61 1.16e+00 7.43e-01 1.58e+01 angle pdb=" N PRO A 247 " pdb=" CD PRO A 247 " pdb=" CG PRO A 247 " ideal model delta sigma weight residual 103.20 97.32 5.88 1.50e+00 4.44e-01 1.54e+01 ... (remaining 7828 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.44: 3067 35.44 - 70.88: 304 70.88 - 106.32: 20 106.32 - 141.76: 0 141.76 - 177.20: 2 Dihedral angle restraints: 3393 sinusoidal: 1953 harmonic: 1440 Sorted by residual: dihedral pdb=" O4' C B 8 " pdb=" C1' C B 8 " pdb=" N1 C B 8 " pdb=" C2 C B 8 " ideal model delta sinusoidal sigma weight residual 232.00 54.80 177.20 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U B -9 " pdb=" C1' U B -9 " pdb=" N1 U B -9 " pdb=" C2 U B -9 " ideal model delta sinusoidal sigma weight residual 232.00 65.11 166.89 1 1.70e+01 3.46e-03 6.56e+01 dihedral pdb=" CA PRO A 295 " pdb=" C PRO A 295 " pdb=" N ILE A 296 " pdb=" CA ILE A 296 " ideal model delta harmonic sigma weight residual 180.00 161.42 18.58 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 3390 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 834 0.080 - 0.159: 63 0.159 - 0.239: 0 0.239 - 0.319: 0 0.319 - 0.398: 1 Chirality restraints: 898 Sorted by residual: chirality pdb=" P C B 8 " pdb=" OP1 C B 8 " pdb=" OP2 C B 8 " pdb=" O5' C B 8 " both_signs ideal model delta sigma weight residual True 2.41 -2.81 -0.40 2.00e-01 2.50e+01 3.97e+00 chirality pdb=" C2' C B 8 " pdb=" C3' C B 8 " pdb=" O2' C B 8 " pdb=" C1' C B 8 " both_signs ideal model delta sigma weight residual False -2.52 -2.68 0.16 2.00e-01 2.50e+01 6.22e-01 chirality pdb=" CA ILE A 419 " pdb=" N ILE A 419 " pdb=" C ILE A 419 " pdb=" CB ILE A 419 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.54e-01 ... (remaining 895 not shown) Planarity restraints: 775 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 242 " 0.060 5.00e-02 4.00e+02 9.03e-02 1.31e+01 pdb=" N PRO A 243 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO A 243 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 243 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C B -5 " -0.027 2.00e-02 2.50e+03 1.49e-02 4.98e+00 pdb=" N1 C B -5 " 0.034 2.00e-02 2.50e+03 pdb=" C2 C B -5 " 0.005 2.00e-02 2.50e+03 pdb=" O2 C B -5 " -0.001 2.00e-02 2.50e+03 pdb=" N3 C B -5 " -0.003 2.00e-02 2.50e+03 pdb=" C4 C B -5 " 0.002 2.00e-02 2.50e+03 pdb=" N4 C B -5 " -0.009 2.00e-02 2.50e+03 pdb=" C5 C B -5 " -0.003 2.00e-02 2.50e+03 pdb=" C6 C B -5 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A 75 " -0.031 5.00e-02 4.00e+02 4.64e-02 3.45e+00 pdb=" N PRO A 76 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 76 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 76 " -0.026 5.00e-02 4.00e+02 ... (remaining 772 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 266 2.71 - 3.25: 4939 3.25 - 3.80: 9255 3.80 - 4.35: 11477 4.35 - 4.90: 17293 Nonbonded interactions: 43230 Sorted by model distance: nonbonded pdb=" OD1 ASP A 185 " pdb=" N GLY A 186 " model vdw 2.156 3.120 nonbonded pdb=" O2' U B -10 " pdb=" O2 U B -9 " model vdw 2.211 3.040 nonbonded pdb=" ND2 ASN A 56 " pdb=" O HIS A 360 " model vdw 2.226 3.120 nonbonded pdb=" OG1 THR A 394 " pdb=" N ASN A 395 " model vdw 2.232 3.120 nonbonded pdb=" OH TYR A 209 " pdb=" O HIS A 214 " model vdw 2.246 3.040 ... (remaining 43225 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: 4.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.820 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:0.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 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 : 0.005 0.043 5569 Z= 0.223 Angle : 0.667 11.764 7833 Z= 0.360 Chirality : 0.043 0.398 898 Planarity : 0.006 0.090 775 Dihedral : 22.785 177.199 2461 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 0.47 % Allowed : 30.02 % Favored : 69.50 % 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: -0.52 (0.38), residues: 492 helix: 0.38 (0.34), residues: 224 sheet: -0.54 (0.76), residues: 54 loop : -1.00 (0.45), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 111 TYR 0.016 0.002 TYR A 317 PHE 0.006 0.001 PHE A 102 TRP 0.015 0.002 TRP A 552 HIS 0.005 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 5569) covalent geometry : angle 0.66653 ( 7833) hydrogen bonds : bond 0.16323 ( 233) hydrogen bonds : angle 5.55970 ( 613) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 96 time to evaluate : 0.179 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 98 average time/residue: 0.1042 time to fit residues: 12.4325 Evaluate side-chains 95 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.1980 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN A 395 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.134035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.111124 restraints weight = 7858.611| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.68 r_work: 0.3269 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.0761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5569 Z= 0.195 Angle : 0.612 7.453 7833 Z= 0.321 Chirality : 0.042 0.173 898 Planarity : 0.006 0.069 775 Dihedral : 23.375 178.955 1447 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 4.02 % Allowed : 27.42 % Favored : 68.56 % 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: -0.09 (0.38), residues: 492 helix: 0.97 (0.34), residues: 213 sheet: -0.29 (0.77), residues: 54 loop : -0.97 (0.43), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 310 TYR 0.016 0.002 TYR A 432 PHE 0.007 0.001 PHE A 350 TRP 0.014 0.002 TRP A 318 HIS 0.005 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 5569) covalent geometry : angle 0.61240 ( 7833) hydrogen bonds : bond 0.04867 ( 233) hydrogen bonds : angle 3.98695 ( 613) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.107 Fit side-chains REVERT: A 195 ASN cc_start: 0.7800 (t0) cc_final: 0.7521 (t0) REVERT: A 197 SER cc_start: 0.8488 (m) cc_final: 0.8272 (m) REVERT: A 280 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6653 (tp) REVERT: A 282 GLU cc_start: 0.7593 (tp30) cc_final: 0.7225 (tp30) REVERT: A 383 HIS cc_start: 0.5672 (OUTLIER) cc_final: 0.5165 (t-90) REVERT: A 395 ASN cc_start: 0.5736 (OUTLIER) cc_final: 0.5098 (p0) REVERT: A 582 GLU cc_start: 0.6901 (mp0) cc_final: 0.6276 (mp0) REVERT: A 647 ILE cc_start: 0.7459 (mt) cc_final: 0.7221 (pt) outliers start: 17 outliers final: 6 residues processed: 120 average time/residue: 0.1087 time to fit residues: 15.6469 Evaluate side-chains 118 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 402 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 51 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN A 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.133860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.110891 restraints weight = 7768.141| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.66 r_work: 0.3266 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5569 Z= 0.206 Angle : 0.614 7.710 7833 Z= 0.322 Chirality : 0.042 0.168 898 Planarity : 0.006 0.060 775 Dihedral : 23.258 177.500 1447 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 4.73 % Allowed : 28.13 % Favored : 67.14 % 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 aren not related in a simple way. whole: -0.09 (0.38), residues: 492 helix: 1.09 (0.34), residues: 212 sheet: -0.34 (0.73), residues: 55 loop : -1.10 (0.42), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 573 TYR 0.016 0.002 TYR A 432 PHE 0.007 0.001 PHE A 350 TRP 0.014 0.002 TRP A 318 HIS 0.013 0.002 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00458 ( 5569) covalent geometry : angle 0.61368 ( 7833) hydrogen bonds : bond 0.04641 ( 233) hydrogen bonds : angle 3.88015 ( 613) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.184 Fit side-chains REVERT: A 195 ASN cc_start: 0.7741 (t0) cc_final: 0.7458 (t0) REVERT: A 197 SER cc_start: 0.8485 (m) cc_final: 0.8222 (m) REVERT: A 271 ARG cc_start: 0.7839 (ptt-90) cc_final: 0.7574 (ptt-90) REVERT: A 280 LEU cc_start: 0.7171 (OUTLIER) cc_final: 0.6663 (tp) REVERT: A 345 ARG cc_start: 0.8155 (mtt-85) cc_final: 0.7939 (mtt-85) REVERT: A 383 HIS cc_start: 0.5743 (OUTLIER) cc_final: 0.5327 (t-90) REVERT: A 582 GLU cc_start: 0.6920 (mp0) cc_final: 0.6289 (mp0) REVERT: A 647 ILE cc_start: 0.7429 (mt) cc_final: 0.7221 (pt) outliers start: 20 outliers final: 11 residues processed: 116 average time/residue: 0.1186 time to fit residues: 16.2893 Evaluate side-chains 115 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 638 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.4980 chunk 53 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 22 optimal weight: 0.0050 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 23 optimal weight: 0.0570 chunk 35 optimal weight: 2.9990 overall best weight: 0.4912 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN ** A 395 ASN ** 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 = 0.3719 r_free = 0.3719 target = 0.135673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.112976 restraints weight = 7857.384| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.63 r_work: 0.3299 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5569 Z= 0.164 Angle : 0.573 7.459 7833 Z= 0.299 Chirality : 0.040 0.162 898 Planarity : 0.006 0.055 775 Dihedral : 23.110 179.100 1447 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 5.20 % Allowed : 28.37 % Favored : 66.43 % 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: 0.17 (0.38), residues: 492 helix: 1.34 (0.35), residues: 212 sheet: -0.25 (0.72), residues: 55 loop : -0.98 (0.42), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 345 TYR 0.015 0.002 TYR A 432 PHE 0.007 0.001 PHE A 350 TRP 0.013 0.001 TRP A 318 HIS 0.012 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 5569) covalent geometry : angle 0.57328 ( 7833) hydrogen bonds : bond 0.04165 ( 233) hydrogen bonds : angle 3.71256 ( 613) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.174 Fit side-chains REVERT: A 271 ARG cc_start: 0.7808 (ptt-90) cc_final: 0.7592 (ptt-90) REVERT: A 280 LEU cc_start: 0.7077 (OUTLIER) cc_final: 0.6636 (tp) REVERT: A 308 ASP cc_start: 0.7829 (t0) cc_final: 0.7599 (t70) REVERT: A 582 GLU cc_start: 0.6927 (mp0) cc_final: 0.6326 (mp0) REVERT: A 585 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.7379 (ttp-110) outliers start: 22 outliers final: 13 residues processed: 119 average time/residue: 0.1114 time to fit residues: 15.8263 Evaluate side-chains 116 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 585 ARG Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 638 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 0.0670 chunk 5 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN A 99 ASN A 203 GLN A 395 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.134400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.111592 restraints weight = 7921.386| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.65 r_work: 0.3279 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 5569 Z= 0.213 Angle : 0.614 7.511 7833 Z= 0.323 Chirality : 0.042 0.169 898 Planarity : 0.006 0.053 775 Dihedral : 23.136 177.416 1447 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 7.33 % Allowed : 26.24 % Favored : 66.43 % 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: 0.09 (0.38), residues: 492 helix: 1.11 (0.35), residues: 219 sheet: -0.19 (0.72), residues: 55 loop : -0.93 (0.42), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 573 TYR 0.016 0.002 TYR A 432 PHE 0.008 0.001 PHE A 137 TRP 0.013 0.002 TRP A 318 HIS 0.010 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 5569) covalent geometry : angle 0.61433 ( 7833) hydrogen bonds : bond 0.04469 ( 233) hydrogen bonds : angle 3.81148 ( 613) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 0.175 Fit side-chains REVERT: A 95 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7303 (pt0) REVERT: A 271 ARG cc_start: 0.7828 (ptt-90) cc_final: 0.7561 (ptt-90) REVERT: A 276 ARG cc_start: 0.7340 (ttm170) cc_final: 0.6813 (mtt90) REVERT: A 280 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6520 (tp) REVERT: A 282 GLU cc_start: 0.7612 (tp30) cc_final: 0.7286 (tp30) REVERT: A 552 TRP cc_start: 0.7339 (OUTLIER) cc_final: 0.6533 (m100) REVERT: A 582 GLU cc_start: 0.6913 (mp0) cc_final: 0.6345 (mp0) REVERT: A 585 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.7356 (ttp-110) REVERT: A 588 GLN cc_start: 0.8117 (mp10) cc_final: 0.7801 (mp10) outliers start: 31 outliers final: 19 residues processed: 129 average time/residue: 0.1193 time to fit residues: 18.3131 Evaluate side-chains 129 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 418 GLN Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain A residue 585 ARG Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 636 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 26 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 20.0000 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 138 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.133164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.110390 restraints weight = 7844.388| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.63 r_work: 0.3269 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 5569 Z= 0.263 Angle : 0.642 7.735 7833 Z= 0.337 Chirality : 0.044 0.177 898 Planarity : 0.006 0.054 775 Dihedral : 23.150 176.813 1447 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 6.15 % Allowed : 26.95 % Favored : 66.90 % 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: -0.03 (0.38), residues: 492 helix: 0.98 (0.34), residues: 219 sheet: -0.26 (0.71), residues: 55 loop : -0.96 (0.42), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 345 TYR 0.017 0.002 TYR A 432 PHE 0.008 0.002 PHE A 137 TRP 0.014 0.002 TRP A 318 HIS 0.010 0.002 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00586 ( 5569) covalent geometry : angle 0.64193 ( 7833) hydrogen bonds : bond 0.04800 ( 233) hydrogen bonds : angle 3.89007 ( 613) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.173 Fit side-chains REVERT: A 95 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7323 (pt0) REVERT: A 276 ARG cc_start: 0.7322 (ttm170) cc_final: 0.6908 (mtt90) REVERT: A 280 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6636 (tp) REVERT: A 552 TRP cc_start: 0.7377 (OUTLIER) cc_final: 0.6529 (m100) REVERT: A 582 GLU cc_start: 0.6919 (mp0) cc_final: 0.6362 (mp0) REVERT: A 585 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.7344 (ttp-110) REVERT: A 588 GLN cc_start: 0.8116 (mp10) cc_final: 0.7810 (mp10) outliers start: 26 outliers final: 19 residues processed: 121 average time/residue: 0.1184 time to fit residues: 17.0771 Evaluate side-chains 124 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 418 GLN Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain A residue 585 ARG Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 636 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 53 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 6 optimal weight: 0.3980 chunk 28 optimal weight: 0.5980 chunk 17 optimal weight: 0.3980 chunk 38 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 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 56 ASN A 395 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.134579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.111746 restraints weight = 7933.918| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.65 r_work: 0.3277 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5569 Z= 0.202 Angle : 0.607 7.537 7833 Z= 0.317 Chirality : 0.041 0.166 898 Planarity : 0.006 0.053 775 Dihedral : 23.087 177.265 1447 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 6.38 % Allowed : 27.66 % Favored : 65.96 % 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: 0.12 (0.38), residues: 492 helix: 1.13 (0.35), residues: 219 sheet: -0.18 (0.72), residues: 55 loop : -0.90 (0.42), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 251 TYR 0.016 0.002 TYR A 432 PHE 0.006 0.001 PHE A 350 TRP 0.014 0.002 TRP A 318 HIS 0.009 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 5569) covalent geometry : angle 0.60674 ( 7833) hydrogen bonds : bond 0.04472 ( 233) hydrogen bonds : angle 3.79797 ( 613) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.153 Fit side-chains REVERT: A 95 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7329 (pt0) REVERT: A 276 ARG cc_start: 0.7312 (ttm170) cc_final: 0.6928 (mtt90) REVERT: A 280 LEU cc_start: 0.7144 (OUTLIER) cc_final: 0.6630 (tp) REVERT: A 395 ASN cc_start: 0.6027 (OUTLIER) cc_final: 0.5306 (p0) REVERT: A 552 TRP cc_start: 0.7355 (OUTLIER) cc_final: 0.6538 (m100) REVERT: A 582 GLU cc_start: 0.6919 (mp0) cc_final: 0.6340 (mp0) REVERT: A 585 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.7340 (ttp-110) outliers start: 27 outliers final: 18 residues processed: 122 average time/residue: 0.1125 time to fit residues: 16.2861 Evaluate side-chains 125 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain A residue 585 ARG Chi-restraints excluded: chain A residue 636 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 39 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 28 optimal weight: 0.4980 chunk 29 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 31 optimal weight: 0.0010 chunk 5 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 0 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 138 ASN A 395 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.135381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.112863 restraints weight = 7849.418| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.60 r_work: 0.3302 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5569 Z= 0.160 Angle : 0.584 7.343 7833 Z= 0.304 Chirality : 0.040 0.163 898 Planarity : 0.006 0.053 775 Dihedral : 23.036 178.062 1447 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.74 % Favored : 91.06 % Rotamer: Outliers : 6.38 % Allowed : 28.13 % Favored : 65.48 % 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: 0.30 (0.38), residues: 492 helix: 1.30 (0.35), residues: 219 sheet: -0.17 (0.73), residues: 55 loop : -0.80 (0.43), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 251 TYR 0.015 0.002 TYR A 432 PHE 0.006 0.001 PHE A 350 TRP 0.015 0.001 TRP A 318 HIS 0.007 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 5569) covalent geometry : angle 0.58415 ( 7833) hydrogen bonds : bond 0.04205 ( 233) hydrogen bonds : angle 3.65485 ( 613) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.169 Fit side-chains REVERT: A 95 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7278 (pt0) REVERT: A 276 ARG cc_start: 0.7310 (ttm170) cc_final: 0.6930 (mtt90) REVERT: A 280 LEU cc_start: 0.7073 (OUTLIER) cc_final: 0.6594 (tp) REVERT: A 308 ASP cc_start: 0.7819 (t0) cc_final: 0.7594 (t70) REVERT: A 395 ASN cc_start: 0.5780 (OUTLIER) cc_final: 0.5193 (p0) REVERT: A 552 TRP cc_start: 0.7323 (OUTLIER) cc_final: 0.6469 (m100) REVERT: A 582 GLU cc_start: 0.6910 (mp0) cc_final: 0.6264 (mp0) outliers start: 27 outliers final: 18 residues processed: 120 average time/residue: 0.1068 time to fit residues: 15.4599 Evaluate side-chains 123 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 418 GLN Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 552 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 47 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 6 optimal weight: 0.2980 chunk 8 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 19 optimal weight: 0.0570 chunk 49 optimal weight: 1.9990 chunk 39 optimal weight: 0.3980 chunk 44 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.136152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.113606 restraints weight = 7870.245| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.61 r_work: 0.3311 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5569 Z= 0.148 Angle : 0.581 7.262 7833 Z= 0.301 Chirality : 0.039 0.162 898 Planarity : 0.006 0.052 775 Dihedral : 22.994 178.286 1447 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.15 % Favored : 90.65 % Rotamer: Outliers : 5.67 % Allowed : 28.84 % Favored : 65.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.38), residues: 492 helix: 1.50 (0.35), residues: 216 sheet: -0.22 (0.73), residues: 55 loop : -0.90 (0.43), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 154 TYR 0.015 0.002 TYR A 432 PHE 0.006 0.001 PHE A 350 TRP 0.015 0.001 TRP A 318 HIS 0.007 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 5569) covalent geometry : angle 0.58100 ( 7833) hydrogen bonds : bond 0.04080 ( 233) hydrogen bonds : angle 3.57938 ( 613) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.174 Fit side-chains REVERT: A 95 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7260 (pt0) REVERT: A 276 ARG cc_start: 0.7304 (ttm170) cc_final: 0.6927 (mtt90) REVERT: A 280 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6590 (tp) REVERT: A 308 ASP cc_start: 0.7827 (t0) cc_final: 0.7624 (t70) REVERT: A 582 GLU cc_start: 0.6940 (mp0) cc_final: 0.6294 (mp0) outliers start: 24 outliers final: 18 residues processed: 118 average time/residue: 0.1136 time to fit residues: 16.0990 Evaluate side-chains 124 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 418 GLN Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 638 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.133738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.110667 restraints weight = 7828.998| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.65 r_work: 0.3266 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5569 Z= 0.231 Angle : 0.631 7.502 7833 Z= 0.329 Chirality : 0.043 0.163 898 Planarity : 0.006 0.052 775 Dihedral : 23.136 177.113 1447 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 5.44 % Allowed : 30.26 % Favored : 64.30 % 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: 0.15 (0.38), residues: 492 helix: 1.15 (0.34), residues: 219 sheet: -0.22 (0.74), residues: 55 loop : -0.86 (0.42), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 251 TYR 0.018 0.002 TYR A 317 PHE 0.016 0.002 PHE A 352 TRP 0.012 0.002 TRP A 318 HIS 0.007 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00515 ( 5569) covalent geometry : angle 0.63064 ( 7833) hydrogen bonds : bond 0.04632 ( 233) hydrogen bonds : angle 3.76412 ( 613) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.144 Fit side-chains REVERT: A 95 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7099 (pt0) REVERT: A 276 ARG cc_start: 0.7270 (ttm170) cc_final: 0.6894 (mtt90) REVERT: A 280 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6610 (tp) REVERT: A 395 ASN cc_start: 0.5848 (OUTLIER) cc_final: 0.5388 (p0) REVERT: A 465 MET cc_start: 0.4779 (tmm) cc_final: 0.4572 (tmm) REVERT: A 552 TRP cc_start: 0.7352 (OUTLIER) cc_final: 0.6506 (m100) REVERT: A 582 GLU cc_start: 0.6974 (mp0) cc_final: 0.6327 (mp0) REVERT: A 588 GLN cc_start: 0.8125 (mp10) cc_final: 0.7829 (mp10) outliers start: 23 outliers final: 15 residues processed: 117 average time/residue: 0.1149 time to fit residues: 16.1882 Evaluate side-chains 120 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain A residue 636 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 42 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 46 optimal weight: 0.0970 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.0670 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 GLN A 395 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.134739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.111768 restraints weight = 7808.910| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.63 r_work: 0.3283 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 5569 Z= 0.164 Angle : 0.609 7.223 7833 Z= 0.318 Chirality : 0.040 0.151 898 Planarity : 0.006 0.053 775 Dihedral : 23.107 177.614 1447 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 5.20 % Allowed : 30.97 % Favored : 63.83 % 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: 0.23 (0.38), residues: 492 helix: 1.37 (0.35), residues: 213 sheet: -0.17 (0.73), residues: 54 loop : -0.96 (0.42), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 271 TYR 0.016 0.002 TYR A 432 PHE 0.015 0.001 PHE A 352 TRP 0.014 0.002 TRP A 318 HIS 0.007 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 5569) covalent geometry : angle 0.60931 ( 7833) hydrogen bonds : bond 0.04294 ( 233) hydrogen bonds : angle 3.69379 ( 613) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1725.09 seconds wall clock time: 30 minutes 9.57 seconds (1809.57 seconds total)