Starting phenix.real_space_refine on Tue Feb 11 12:52:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iew_35374/02_2025/8iew_35374.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iew_35374/02_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_35374/02_2025/8iew_35374.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iew_35374/02_2025/8iew_35374.map" model { file = "/net/cci-nas-00/data/ceres_data/8iew_35374/02_2025/8iew_35374.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iew_35374/02_2025/8iew_35374.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 4.64, per 1000 atoms: 0.87 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: 1.64 Conformation dependent library (CDL) restraints added in 650.3 milliseconds 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: 1.91 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: 2.17 Time building geometry restraints manager: 1.84 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: 2.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.130 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.360 ------------------------------------------------------------------------------- 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= 0.295 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (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 TRP 0.015 0.002 TRP A 552 HIS 0.005 0.001 HIS A 214 PHE 0.006 0.001 PHE A 102 TYR 0.016 0.002 TYR A 317 ARG 0.005 0.001 ARG A 111 *********************** 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 : 0.512 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 98 average time/residue: 0.2560 time to fit residues: 30.2470 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 : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.5980 chunk 40 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 ** 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 = 0.3680 r_free = 0.3680 target = 0.133094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.110205 restraints weight = 7728.267| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.67 r_work: 0.3256 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.0720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5569 Z= 0.335 Angle : 0.641 7.675 7833 Z= 0.337 Chirality : 0.043 0.177 898 Planarity : 0.006 0.068 775 Dihedral : 23.454 177.602 1447 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 4.26 % Allowed : 27.42 % Favored : 68.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.38), residues: 492 helix: 0.82 (0.34), residues: 213 sheet: -0.32 (0.77), residues: 54 loop : -1.02 (0.43), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 318 HIS 0.005 0.001 HIS A 214 PHE 0.007 0.001 PHE A 102 TYR 0.017 0.002 TYR A 432 ARG 0.004 0.000 ARG A 345 *********************** 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 124 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.503 Fit side-chains REVERT: A 280 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6646 (tp) REVERT: A 282 GLU cc_start: 0.7577 (tp30) cc_final: 0.7213 (tp30) REVERT: A 582 GLU cc_start: 0.6890 (mp0) cc_final: 0.6265 (mp0) REVERT: A 588 GLN cc_start: 0.8100 (mp10) cc_final: 0.7791 (mp10) REVERT: A 647 ILE cc_start: 0.7469 (mt) cc_final: 0.7244 (pt) outliers start: 18 outliers final: 9 residues processed: 117 average time/residue: 0.2522 time to fit residues: 35.5032 Evaluate side-chains 114 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN 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 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 402 SER Chi-restraints excluded: chain A residue 636 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 12 optimal weight: 0.0060 chunk 31 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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 = 0.3694 r_free = 0.3694 target = 0.133949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.111055 restraints weight = 7781.658| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.66 r_work: 0.3267 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.0967 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= 0.265 Angle : 0.601 7.488 7833 Z= 0.314 Chirality : 0.041 0.161 898 Planarity : 0.006 0.060 775 Dihedral : 23.241 177.817 1447 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 4.49 % Allowed : 27.90 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.38), residues: 492 helix: 1.09 (0.35), residues: 213 sheet: -0.31 (0.73), residues: 55 loop : -1.07 (0.42), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 318 HIS 0.008 0.001 HIS A 214 PHE 0.007 0.001 PHE A 350 TYR 0.016 0.002 TYR A 432 ARG 0.004 0.000 ARG A 573 *********************** 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 125 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.402 Fit side-chains REVERT: A 195 ASN cc_start: 0.7759 (t0) cc_final: 0.7528 (t0) REVERT: A 260 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7656 (ttt180) REVERT: A 271 ARG cc_start: 0.7835 (ptt-90) cc_final: 0.7578 (ptt-90) REVERT: A 280 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6701 (tp) REVERT: A 345 ARG cc_start: 0.8135 (mtt-85) cc_final: 0.7930 (mtt-85) REVERT: A 383 HIS cc_start: 0.5658 (OUTLIER) cc_final: 0.5292 (t-90) REVERT: A 582 GLU cc_start: 0.6910 (mp0) cc_final: 0.6283 (mp0) REVERT: A 647 ILE cc_start: 0.7422 (mt) cc_final: 0.7215 (pt) outliers start: 19 outliers final: 10 residues processed: 118 average time/residue: 0.2525 time to fit residues: 35.5888 Evaluate side-chains 117 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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 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 260 ARG 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 420 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 1 optimal weight: 0.0050 chunk 8 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 3 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.6394 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.134711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.112092 restraints weight = 7897.715| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.62 r_work: 0.3282 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1065 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= 0.275 Angle : 0.599 7.473 7833 Z= 0.313 Chirality : 0.041 0.155 898 Planarity : 0.006 0.056 775 Dihedral : 23.200 178.047 1447 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.38), residues: 492 helix: 1.01 (0.34), residues: 219 sheet: -0.32 (0.72), residues: 55 loop : -0.96 (0.43), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 318 HIS 0.011 0.001 HIS A 214 PHE 0.007 0.001 PHE A 350 TYR 0.016 0.002 TYR A 432 ARG 0.003 0.000 ARG A 251 *********************** 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 137 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 106 time to evaluate : 0.504 Fit side-chains REVERT: A 95 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7092 (pt0) REVERT: A 260 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7690 (ttt180) REVERT: A 271 ARG cc_start: 0.7827 (ptt-90) cc_final: 0.7585 (ptt-90) REVERT: A 280 LEU cc_start: 0.7134 (OUTLIER) cc_final: 0.6539 (tp) REVERT: A 282 GLU cc_start: 0.7574 (tp30) cc_final: 0.7274 (tp30) REVERT: A 552 TRP cc_start: 0.7336 (OUTLIER) cc_final: 0.6507 (m100) REVERT: A 582 GLU cc_start: 0.6919 (mp0) cc_final: 0.6348 (mp0) REVERT: A 585 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.7367 (ttp-110) outliers start: 31 outliers final: 18 residues processed: 126 average time/residue: 0.2556 time to fit residues: 38.3695 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 : 0.466 ------------------------------------------------------------------------------- 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 246 VAL Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 260 ARG Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 292 GLU 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 411 LEU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 552 TRP Chi-restraints excluded: chain A residue 585 ARG 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 36 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.3689 r_free = 0.3689 target = 0.133338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.110756 restraints weight = 7804.692| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.63 r_work: 0.3263 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 5569 Z= 0.371 Angle : 0.659 8.682 7833 Z= 0.344 Chirality : 0.044 0.155 898 Planarity : 0.006 0.055 775 Dihedral : 23.233 176.809 1447 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 7.33 % Allowed : 26.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.38), residues: 492 helix: 0.88 (0.34), residues: 219 sheet: -0.48 (0.72), residues: 58 loop : -0.94 (0.43), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 318 HIS 0.014 0.002 HIS A 214 PHE 0.008 0.002 PHE A 350 TYR 0.017 0.002 TYR A 432 ARG 0.004 0.000 ARG A 345 *********************** 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 135 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 0.504 Fit side-chains REVERT: A 95 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7093 (pt0) REVERT: A 271 ARG cc_start: 0.7837 (ptt-90) cc_final: 0.7585 (ptt-90) REVERT: A 280 LEU cc_start: 0.7193 (OUTLIER) cc_final: 0.6582 (tp) REVERT: A 282 GLU cc_start: 0.7610 (tp30) cc_final: 0.7282 (tp30) REVERT: A 552 TRP cc_start: 0.7364 (OUTLIER) cc_final: 0.6526 (m100) REVERT: A 582 GLU cc_start: 0.6931 (mp0) cc_final: 0.6356 (mp0) REVERT: A 585 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7361 (ttp-110) REVERT: A 588 GLN cc_start: 0.8108 (mp10) cc_final: 0.7810 (mp10) outliers start: 31 outliers final: 21 residues processed: 125 average time/residue: 0.2564 time to fit residues: 38.2705 Evaluate side-chains 128 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.518 ------------------------------------------------------------------------------- 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 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 292 GLU 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 420 VAL 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 2 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 0.0470 chunk 6 optimal weight: 0.0370 chunk 7 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 32 optimal weight: 0.3980 chunk 3 optimal weight: 0.4980 chunk 48 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 overall best weight: 0.3156 ------------------------------------------------------------------------------- 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 395 ASN ** 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 = 0.3731 r_free = 0.3731 target = 0.136410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.114113 restraints weight = 7821.523| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.61 r_work: 0.3313 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5569 Z= 0.188 Angle : 0.568 7.260 7833 Z= 0.296 Chirality : 0.039 0.149 898 Planarity : 0.005 0.053 775 Dihedral : 22.984 179.187 1447 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 4.26 % Allowed : 29.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.39), residues: 492 helix: 1.46 (0.35), residues: 218 sheet: -0.24 (0.71), residues: 55 loop : -0.98 (0.43), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 249 HIS 0.010 0.001 HIS A 214 PHE 0.006 0.001 PHE A 350 TYR 0.015 0.001 TYR A 432 ARG 0.003 0.000 ARG A 573 *********************** 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 122 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.475 Fit side-chains REVERT: A 271 ARG cc_start: 0.7793 (ptt-90) cc_final: 0.7587 (ptt-90) REVERT: A 280 LEU cc_start: 0.7038 (OUTLIER) cc_final: 0.6533 (tp) REVERT: A 282 GLU cc_start: 0.7596 (tp30) cc_final: 0.7290 (tp30) REVERT: A 582 GLU cc_start: 0.6929 (mp0) cc_final: 0.6260 (mp0) outliers start: 18 outliers final: 10 residues processed: 117 average time/residue: 0.2475 time to fit residues: 34.8227 Evaluate side-chains 114 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 118 VAL 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 256 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 638 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 0.0970 chunk 31 optimal weight: 0.0060 chunk 40 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 395 ASN ** 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 = 0.3722 r_free = 0.3722 target = 0.135733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.113218 restraints weight = 7822.956| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.62 r_work: 0.3302 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1426 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= 0.224 Angle : 0.577 7.484 7833 Z= 0.300 Chirality : 0.039 0.147 898 Planarity : 0.006 0.052 775 Dihedral : 22.982 178.413 1447 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 5.44 % Allowed : 28.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.39), residues: 492 helix: 1.52 (0.35), residues: 216 sheet: -0.15 (0.72), residues: 55 loop : -0.92 (0.43), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 318 HIS 0.010 0.001 HIS A 214 PHE 0.007 0.001 PHE A 350 TYR 0.016 0.002 TYR A 432 ARG 0.005 0.000 ARG A 573 *********************** 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 131 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.496 Fit side-chains REVERT: A 95 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.6999 (pt0) REVERT: A 276 ARG cc_start: 0.7287 (ttm170) cc_final: 0.6881 (mtt90) REVERT: A 280 LEU cc_start: 0.7071 (OUTLIER) cc_final: 0.6493 (tp) REVERT: A 282 GLU cc_start: 0.7601 (tp30) cc_final: 0.7308 (tp30) REVERT: A 582 GLU cc_start: 0.6922 (mp0) cc_final: 0.6285 (mp0) outliers start: 23 outliers final: 15 residues processed: 123 average time/residue: 0.2501 time to fit residues: 36.7828 Evaluate side-chains 123 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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 180 THR 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 327 SER 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 418 GLN Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 425 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 37 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 36 optimal weight: 0.2980 chunk 24 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 0.0980 chunk 46 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3722 r_free = 0.3722 target = 0.135670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.113144 restraints weight = 7837.537| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.62 r_work: 0.3302 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.1477 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= 0.238 Angle : 0.585 7.617 7833 Z= 0.304 Chirality : 0.040 0.147 898 Planarity : 0.006 0.051 775 Dihedral : 22.986 178.688 1447 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 4.73 % Allowed : 30.02 % Favored : 65.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.38), residues: 492 helix: 1.52 (0.35), residues: 213 sheet: -0.22 (0.73), residues: 55 loop : -0.88 (0.42), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 318 HIS 0.010 0.001 HIS A 214 PHE 0.007 0.001 PHE A 350 TYR 0.020 0.002 TYR A 87 ARG 0.004 0.000 ARG A 573 *********************** 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 127 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.396 Fit side-chains REVERT: A 95 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7023 (pt0) REVERT: A 276 ARG cc_start: 0.7298 (ttm170) cc_final: 0.6927 (mtt90) REVERT: A 280 LEU cc_start: 0.7074 (OUTLIER) cc_final: 0.6521 (tp) REVERT: A 282 GLU cc_start: 0.7605 (tp30) cc_final: 0.7310 (tp30) REVERT: A 582 GLU cc_start: 0.6950 (mp0) cc_final: 0.6295 (mp0) REVERT: A 588 GLN cc_start: 0.8124 (mp10) cc_final: 0.7839 (mp10) outliers start: 20 outliers final: 15 residues processed: 119 average time/residue: 0.2523 time to fit residues: 35.8905 Evaluate side-chains 123 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.518 ------------------------------------------------------------------------------- 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 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 327 SER 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 418 GLN Chi-restraints excluded: chain A residue 420 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 1 optimal weight: 0.9990 chunk 22 optimal weight: 0.0980 chunk 10 optimal weight: 0.8980 chunk 36 optimal weight: 0.0470 chunk 37 optimal weight: 0.8980 chunk 11 optimal weight: 20.0000 chunk 6 optimal weight: 0.1980 chunk 29 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.3678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 395 ASN ** 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 = 0.3737 r_free = 0.3737 target = 0.136875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.114445 restraints weight = 7824.969| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.62 r_work: 0.3327 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5569 Z= 0.197 Angle : 0.567 7.611 7833 Z= 0.294 Chirality : 0.039 0.150 898 Planarity : 0.006 0.050 775 Dihedral : 22.902 179.320 1447 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 4.02 % Allowed : 31.21 % Favored : 64.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.39), residues: 492 helix: 1.64 (0.35), residues: 216 sheet: -0.27 (0.73), residues: 55 loop : -0.85 (0.43), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 318 HIS 0.008 0.001 HIS A 214 PHE 0.010 0.001 PHE A 352 TYR 0.019 0.002 TYR A 87 ARG 0.003 0.000 ARG A 573 *********************** 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 121 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.486 Fit side-chains REVERT: A 95 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7195 (pt0) REVERT: A 276 ARG cc_start: 0.7284 (ttm170) cc_final: 0.6913 (mtt90) REVERT: A 280 LEU cc_start: 0.7036 (OUTLIER) cc_final: 0.6487 (tp) REVERT: A 282 GLU cc_start: 0.7605 (tp30) cc_final: 0.7326 (tp30) REVERT: A 582 GLU cc_start: 0.6944 (mp0) cc_final: 0.6277 (mp0) REVERT: A 588 GLN cc_start: 0.8123 (mp10) cc_final: 0.7880 (mp10) outliers start: 17 outliers final: 11 residues processed: 116 average time/residue: 0.2613 time to fit residues: 36.6096 Evaluate side-chains 117 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 118 VAL 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 256 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 420 VAL 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 13 optimal weight: 0.0770 chunk 40 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 12 optimal weight: 0.2980 chunk 39 optimal weight: 0.0370 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 395 ASN ** 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 = 0.3743 r_free = 0.3743 target = 0.137299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.114830 restraints weight = 7878.567| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.62 r_work: 0.3332 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5569 Z= 0.194 Angle : 0.565 7.526 7833 Z= 0.292 Chirality : 0.039 0.156 898 Planarity : 0.006 0.050 775 Dihedral : 22.868 179.814 1447 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 4.26 % Allowed : 30.73 % Favored : 65.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.39), residues: 492 helix: 1.73 (0.35), residues: 216 sheet: -0.21 (0.74), residues: 55 loop : -0.81 (0.43), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 318 HIS 0.007 0.001 HIS A 214 PHE 0.008 0.001 PHE A 352 TYR 0.019 0.002 TYR A 87 ARG 0.005 0.000 ARG A 271 ********************** 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 122 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.508 Fit side-chains REVERT: A 95 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7184 (pt0) REVERT: A 276 ARG cc_start: 0.7294 (ttm170) cc_final: 0.6939 (mtt90) REVERT: A 280 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6579 (tp) REVERT: A 420 VAL cc_start: 0.7237 (OUTLIER) cc_final: 0.7024 (p) REVERT: A 465 MET cc_start: 0.4867 (tmm) cc_final: 0.4645 (tmm) REVERT: A 588 GLN cc_start: 0.8136 (mp10) cc_final: 0.7910 (mp10) REVERT: A 637 ASP cc_start: 0.7186 (m-30) cc_final: 0.6947 (m-30) outliers start: 18 outliers final: 13 residues processed: 117 average time/residue: 0.2490 time to fit residues: 35.4061 Evaluate side-chains 120 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN 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 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 327 SER Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 648 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 15 optimal weight: 0.0980 chunk 37 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.135399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.112789 restraints weight = 7869.856| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.63 r_work: 0.3300 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1657 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= 0.282 Angle : 0.602 7.535 7833 Z= 0.314 Chirality : 0.041 0.156 898 Planarity : 0.006 0.050 775 Dihedral : 23.011 178.649 1447 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 4.26 % Allowed : 30.97 % Favored : 64.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.38), residues: 492 helix: 1.52 (0.35), residues: 213 sheet: -0.27 (0.73), residues: 55 loop : -0.88 (0.42), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 318 HIS 0.009 0.001 HIS A 214 PHE 0.013 0.002 PHE A 352 TYR 0.019 0.002 TYR A 87 ARG 0.005 0.000 ARG A 271 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3564.62 seconds wall clock time: 64 minutes 1.17 seconds (3841.17 seconds total)