Starting phenix.real_space_refine on Wed Jul 1 23:52:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hfg_34720/07_2026/8hfg_34720.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hfg_34720/07_2026/8hfg_34720.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hfg_34720/07_2026/8hfg_34720.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hfg_34720/07_2026/8hfg_34720.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hfg_34720/07_2026/8hfg_34720.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hfg_34720/07_2026/8hfg_34720.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.168 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 20 5.16 5 Cl 1 4.86 5 C 2950 2.51 5 N 679 2.21 5 O 744 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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4394 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4366 Classifications: {'peptide': 545} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 525} Chain breaks: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 27 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'LDP': 2} Classifications: {'undetermined': 2, 'water': 5} Link IDs: {None: 5} Chain breaks: 1 Time building chain proxies: 1.17, per 1000 atoms: 0.27 Number of scatterers: 4394 At special positions: 0 Unit cell: (71.445, 68.1975, 96.3425, 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) Cl 1 17.00 S 20 16.00 O 744 8.00 N 679 7.00 C 2950 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 185 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.38 Conformation dependent library (CDL) restraints added in 98.5 milliseconds 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1004 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 1 sheets defined 79.8% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 60 through 73 Processing helix chain 'A' and resid 75 through 89 removed outlier: 3.687A pdb=" N VAL A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N PHE A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Proline residue: A 83 - end of helix Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 105 through 121 Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.594A pdb=" N TRP A 128 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE A 130 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 134 through 166 removed outlier: 4.016A pdb=" N PHE A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N TYR A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL A 154 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE A 156 " --> pdb=" O TYR A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 234 through 253 removed outlier: 3.623A pdb=" N LEU A 239 " --> pdb=" O TRP A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 283 removed outlier: 3.521A pdb=" N THR A 268 " --> pdb=" O TRP A 264 " (cutoff:3.500A) Proline residue: A 270 - end of helix removed outlier: 4.073A pdb=" N THR A 283 " --> pdb=" O VAL A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.803A pdb=" N GLY A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 319 Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 338 through 373 removed outlier: 3.714A pdb=" N ASP A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 397 Proline residue: A 392 - end of helix removed outlier: 3.787A pdb=" N THR A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 435 removed outlier: 3.704A pdb=" N ASP A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 441 Processing helix chain 'A' and resid 441 through 459 Processing helix chain 'A' and resid 464 through 476 removed outlier: 3.731A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 496 Processing helix chain 'A' and resid 497 through 510 Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 551 through 567 removed outlier: 3.848A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TRP A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 580 Processing helix chain 'A' and resid 583 through 593 Processing helix chain 'A' and resid 594 through 598 removed outlier: 3.646A pdb=" N HIS A 598 " --> pdb=" O GLU A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 604 Processing helix chain 'A' and resid 606 through 609 Processing helix chain 'A' and resid 610 through 615 removed outlier: 3.810A pdb=" N TRP A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 544 through 545 289 hydrogen bonds defined for protein. 843 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.43 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 644 1.26 - 1.40: 1311 1.40 - 1.54: 2448 1.54 - 1.68: 96 1.68 - 1.81: 31 Bond restraints: 4530 Sorted by residual: bond pdb=" C LEU A 302 " pdb=" O LEU A 302 " ideal model delta sigma weight residual 1.236 1.121 0.115 1.31e-02 5.83e+03 7.71e+01 bond pdb=" C GLY A 92 " pdb=" O GLY A 92 " ideal model delta sigma weight residual 1.235 1.134 0.100 1.35e-02 5.49e+03 5.53e+01 bond pdb=" C ASN A 89 " pdb=" O ASN A 89 " ideal model delta sigma weight residual 1.236 1.145 0.091 1.47e-02 4.63e+03 3.82e+01 bond pdb=" C ARG A 301 " pdb=" O ARG A 301 " ideal model delta sigma weight residual 1.236 1.159 0.077 1.32e-02 5.74e+03 3.38e+01 bond pdb=" C LYS A 88 " pdb=" O LYS A 88 " ideal model delta sigma weight residual 1.236 1.169 0.067 1.16e-02 7.43e+03 3.33e+01 ... (remaining 4525 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.24: 6105 3.24 - 6.49: 59 6.49 - 9.73: 9 9.73 - 12.97: 3 12.97 - 16.22: 2 Bond angle restraints: 6178 Sorted by residual: angle pdb=" N LEU A 302 " pdb=" CA LEU A 302 " pdb=" C LEU A 302 " ideal model delta sigma weight residual 113.18 99.01 14.17 1.21e+00 6.83e-01 1.37e+02 angle pdb=" N TYR A 300 " pdb=" CA TYR A 300 " pdb=" C TYR A 300 " ideal model delta sigma weight residual 113.28 101.21 12.07 1.22e+00 6.72e-01 9.78e+01 angle pdb=" C ARG A 301 " pdb=" CA ARG A 301 " pdb=" CB ARG A 301 " ideal model delta sigma weight residual 109.55 93.33 16.22 1.68e+00 3.54e-01 9.32e+01 angle pdb=" CA PRO A 83 " pdb=" N PRO A 83 " pdb=" CD PRO A 83 " ideal model delta sigma weight residual 112.00 99.50 12.50 1.40e+00 5.10e-01 7.98e+01 angle pdb=" O TYR A 87 " pdb=" C TYR A 87 " pdb=" N LYS A 88 " ideal model delta sigma weight residual 122.09 113.75 8.34 1.08e+00 8.57e-01 5.97e+01 ... (remaining 6173 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 2205 17.29 - 34.57: 237 34.57 - 51.86: 59 51.86 - 69.15: 16 69.15 - 86.44: 4 Dihedral angle restraints: 2521 sinusoidal: 945 harmonic: 1576 Sorted by residual: dihedral pdb=" C ARG A 301 " pdb=" N ARG A 301 " pdb=" CA ARG A 301 " pdb=" CB ARG A 301 " ideal model delta harmonic sigma weight residual -122.60 -103.73 -18.87 0 2.50e+00 1.60e-01 5.70e+01 dihedral pdb=" CA ILE A 103 " pdb=" C ILE A 103 " pdb=" N ILE A 104 " pdb=" CA ILE A 104 " ideal model delta harmonic sigma weight residual 180.00 -157.88 -22.12 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" C TYR A 205 " pdb=" N TYR A 205 " pdb=" CA TYR A 205 " pdb=" CB TYR A 205 " ideal model delta harmonic sigma weight residual -122.60 -133.40 10.80 0 2.50e+00 1.60e-01 1.87e+01 ... (remaining 2518 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 670 0.095 - 0.189: 14 0.189 - 0.284: 2 0.284 - 0.379: 0 0.379 - 0.474: 1 Chirality restraints: 687 Sorted by residual: chirality pdb=" CA TYR A 205 " pdb=" N TYR A 205 " pdb=" C TYR A 205 " pdb=" CB TYR A 205 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.61e+00 chirality pdb=" CA LYS A 88 " pdb=" N LYS A 88 " pdb=" C LYS A 88 " pdb=" CB LYS A 88 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA ILE A 617 " pdb=" N ILE A 617 " pdb=" C ILE A 617 " pdb=" CB ILE A 617 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.96e-01 ... (remaining 684 not shown) Planarity restraints: 749 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 93 " 0.026 2.00e-02 2.50e+03 5.29e-02 2.80e+01 pdb=" C ALA A 93 " -0.092 2.00e-02 2.50e+03 pdb=" O ALA A 93 " 0.033 2.00e-02 2.50e+03 pdb=" N PHE A 94 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 82 " 0.086 5.00e-02 4.00e+02 1.22e-01 2.39e+01 pdb=" N PRO A 83 " -0.211 5.00e-02 4.00e+02 pdb=" CA PRO A 83 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 83 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 103 " 0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C ILE A 103 " -0.063 2.00e-02 2.50e+03 pdb=" O ILE A 103 " 0.024 2.00e-02 2.50e+03 pdb=" N ILE A 104 " 0.021 2.00e-02 2.50e+03 ... (remaining 746 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 48 2.63 - 3.20: 4094 3.20 - 3.77: 6981 3.77 - 4.33: 9779 4.33 - 4.90: 16616 Nonbonded interactions: 37518 Sorted by model distance: nonbonded pdb=" O HOH A 801 " pdb=" O HOH A 803 " model vdw 2.067 3.040 nonbonded pdb=" O PHE A 577 " pdb=" NH1 ARG A 587 " model vdw 2.146 3.120 nonbonded pdb=" O2 LDP A 701 " pdb=" O HOH A 801 " model vdw 2.253 3.040 nonbonded pdb=" NH1 ARG A 121 " pdb=" O ASN A 333 " model vdw 2.308 3.120 nonbonded pdb=" O GLY A 90 " pdb=" O HOH A 802 " model vdw 2.318 3.040 ... (remaining 37513 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.800 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 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 : 0.006 0.131 4531 Z= 0.392 Angle : 0.804 16.218 6180 Z= 0.503 Chirality : 0.043 0.474 687 Planarity : 0.007 0.122 749 Dihedral : 15.709 86.436 1514 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.15 % Favored : 96.66 % Rotamer: Outliers : 1.96 % Allowed : 15.43 % Favored : 82.61 % Cbeta Deviations : 0.60 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.38), residues: 539 helix: 1.74 (0.28), residues: 362 sheet: None (None), residues: 0 loop : -0.33 (0.50), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 512 TYR 0.019 0.001 TYR A 300 PHE 0.021 0.001 PHE A 299 TRP 0.006 0.001 TRP A 235 HIS 0.006 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.39 ( 4530) covalent geometry : angle 0.80407 / 0.50 ( 6178) SS BOND : bond 0.00181 / 0.11 ( 1) SS BOND : angle 1.24496 / 0.49 ( 2) hydrogen bonds : bond 0.11866 / 7.38 ( 289) hydrogen bonds : angle 5.11628 / 3.62 ( 843) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.146 Fit side-chains REVERT: A 300 TYR cc_start: 0.5510 (OUTLIER) cc_final: 0.5277 (m-10) outliers start: 9 outliers final: 2 residues processed: 86 average time/residue: 0.3579 time to fit residues: 32.4312 Evaluate side-chains 60 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 TYR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 617 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 0.0370 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 19 optimal weight: 0.1980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 ASN A 178 HIS A 280 HIS A 603 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.158776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.132082 restraints weight = 4799.796| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.53 r_work: 0.3301 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.4474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4531 Z= 0.163 Angle : 0.602 7.193 6180 Z= 0.311 Chirality : 0.041 0.142 687 Planarity : 0.005 0.065 749 Dihedral : 6.105 74.583 595 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.70 % Allowed : 17.61 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.37), residues: 539 helix: 1.48 (0.27), residues: 378 sheet: None (None), residues: 0 loop : 0.01 (0.53), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 512 TYR 0.016 0.002 TYR A 84 PHE 0.022 0.002 PHE A 408 TRP 0.024 0.001 TRP A 235 HIS 0.005 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 ( 4530) covalent geometry : angle 0.60155 / 0.31 ( 6178) SS BOND : bond 0.01186 / 0.74 ( 1) SS BOND : angle 0.78961 / 0.38 ( 2) hydrogen bonds : bond 0.04328 / 2.91 ( 289) hydrogen bonds : angle 4.83849 / 3.56 ( 843) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: A 236 GLN cc_start: 0.7869 (mt0) cc_final: 0.7664 (mt0) REVERT: A 296 HIS cc_start: 0.7158 (t70) cc_final: 0.6953 (t70) REVERT: A 310 ASP cc_start: 0.7712 (m-30) cc_final: 0.7403 (t0) REVERT: A 373 LYS cc_start: 0.7638 (mmmm) cc_final: 0.7303 (mmpt) REVERT: A 375 ASN cc_start: 0.7479 (m-40) cc_final: 0.7107 (t0) REVERT: A 431 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7397 (mt) REVERT: A 507 GLN cc_start: 0.8047 (tt0) cc_final: 0.7476 (tt0) REVERT: A 556 TRP cc_start: 0.7230 (m100) cc_final: 0.5969 (m-10) REVERT: A 595 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6970 (mt-10) outliers start: 17 outliers final: 4 residues processed: 95 average time/residue: 0.3360 time to fit residues: 33.8820 Evaluate side-chains 73 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 617 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 42 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 25 optimal weight: 0.2980 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.162118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.134418 restraints weight = 4605.488| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.77 r_work: 0.3399 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.5855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 4531 Z= 0.140 Angle : 0.552 7.074 6180 Z= 0.273 Chirality : 0.039 0.133 687 Planarity : 0.004 0.052 749 Dihedral : 5.435 71.005 592 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.48 % Allowed : 18.26 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.37), residues: 539 helix: 1.66 (0.27), residues: 377 sheet: None (None), residues: 0 loop : 0.03 (0.53), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 587 TYR 0.018 0.002 TYR A 84 PHE 0.010 0.001 PHE A 110 TRP 0.009 0.001 TRP A 235 HIS 0.004 0.001 HIS A 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 4530) covalent geometry : angle 0.55152 / 0.27 ( 6178) SS BOND : bond 0.00856 / 0.54 ( 1) SS BOND : angle 1.77567 / 0.83 ( 2) hydrogen bonds : bond 0.03994 / 2.64 ( 289) hydrogen bonds : angle 4.72818 / 3.49 ( 843) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.150 Fit side-chains revert: symmetry clash REVERT: A 109 LEU cc_start: 0.7805 (mm) cc_final: 0.7494 (mt) REVERT: A 204 LYS cc_start: 0.6614 (OUTLIER) cc_final: 0.6355 (tppp) REVERT: A 296 HIS cc_start: 0.7214 (t70) cc_final: 0.6849 (t70) REVERT: A 310 ASP cc_start: 0.7765 (m-30) cc_final: 0.7553 (m-30) REVERT: A 375 ASN cc_start: 0.7860 (m-40) cc_final: 0.7310 (t0) REVERT: A 377 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7202 (mp0) REVERT: A 403 PHE cc_start: 0.7838 (t80) cc_final: 0.7494 (t80) REVERT: A 431 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7408 (mt) REVERT: A 507 GLN cc_start: 0.7998 (tt0) cc_final: 0.7486 (tt0) REVERT: A 547 ASP cc_start: 0.7475 (p0) cc_final: 0.7219 (m-30) REVERT: A 556 TRP cc_start: 0.7637 (m100) cc_final: 0.6180 (m-10) REVERT: A 584 LEU cc_start: 0.6339 (tp) cc_final: 0.6109 (tp) outliers start: 16 outliers final: 4 residues processed: 83 average time/residue: 0.2520 time to fit residues: 22.5960 Evaluate side-chains 76 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 575 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 32 optimal weight: 6.9990 chunk 24 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 36 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 53 optimal weight: 0.1980 chunk 37 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.160654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.132826 restraints weight = 4607.241| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.73 r_work: 0.3340 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.6960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4531 Z= 0.128 Angle : 0.519 7.045 6180 Z= 0.262 Chirality : 0.039 0.160 687 Planarity : 0.004 0.047 749 Dihedral : 5.309 68.772 590 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.70 % Allowed : 19.13 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.37), residues: 539 helix: 1.74 (0.27), residues: 381 sheet: None (None), residues: 0 loop : 0.08 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 587 TYR 0.018 0.001 TYR A 84 PHE 0.015 0.001 PHE A 409 TRP 0.008 0.001 TRP A 235 HIS 0.004 0.001 HIS A 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 4530) covalent geometry : angle 0.51884 / 0.26 ( 6178) SS BOND : bond 0.00251 / 0.16 ( 1) SS BOND : angle 1.06702 / 0.51 ( 2) hydrogen bonds : bond 0.03891 / 2.62 ( 289) hydrogen bonds : angle 4.71051 / 3.48 ( 843) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.151 Fit side-chains REVERT: A 118 GLN cc_start: 0.8727 (tt0) cc_final: 0.8517 (tt0) REVERT: A 373 LYS cc_start: 0.8022 (mmmm) cc_final: 0.7474 (mtmt) REVERT: A 507 GLN cc_start: 0.8126 (tt0) cc_final: 0.7571 (tt0) REVERT: A 556 TRP cc_start: 0.7870 (m100) cc_final: 0.6475 (m-10) REVERT: A 584 LEU cc_start: 0.6700 (tp) cc_final: 0.6462 (tp) REVERT: A 595 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7319 (mt-10) outliers start: 17 outliers final: 7 residues processed: 74 average time/residue: 0.2993 time to fit residues: 23.6387 Evaluate side-chains 65 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 617 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 11 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 337 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.155891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.129987 restraints weight = 4676.198| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.65 r_work: 0.3336 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.7312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4531 Z= 0.141 Angle : 0.528 7.219 6180 Z= 0.266 Chirality : 0.040 0.165 687 Planarity : 0.004 0.044 749 Dihedral : 5.136 63.181 590 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.91 % Allowed : 19.78 % Favored : 76.30 % 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 are not related in a simple way. whole: 1.81 (0.37), residues: 539 helix: 1.71 (0.27), residues: 379 sheet: None (None), residues: 0 loop : 0.09 (0.51), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 587 TYR 0.020 0.001 TYR A 84 PHE 0.031 0.002 PHE A 408 TRP 0.006 0.001 TRP A 128 HIS 0.003 0.001 HIS A 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 ( 4530) covalent geometry : angle 0.52783 / 0.27 ( 6178) SS BOND : bond 0.00150 / 0.09 ( 1) SS BOND : angle 1.15312 / 0.54 ( 2) hydrogen bonds : bond 0.03987 / 2.66 ( 289) hydrogen bonds : angle 4.76936 / 3.52 ( 843) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.100 Fit side-chains REVERT: A 109 LEU cc_start: 0.7912 (mm) cc_final: 0.7701 (mt) REVERT: A 373 LYS cc_start: 0.8202 (mmmm) cc_final: 0.7608 (mtmt) REVERT: A 418 ASP cc_start: 0.7519 (OUTLIER) cc_final: 0.7030 (m-30) REVERT: A 507 GLN cc_start: 0.8199 (tt0) cc_final: 0.7655 (tt0) REVERT: A 584 LEU cc_start: 0.6666 (tp) cc_final: 0.6464 (tp) REVERT: A 595 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7480 (mt-10) outliers start: 18 outliers final: 9 residues processed: 70 average time/residue: 0.2629 time to fit residues: 19.8006 Evaluate side-chains 67 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 617 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 50 optimal weight: 0.9990 chunk 52 optimal weight: 0.0370 chunk 18 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 337 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.142363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.119697 restraints weight = 4893.311| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.24 r_work: 0.3153 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.7488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4531 Z= 0.133 Angle : 0.529 7.981 6180 Z= 0.263 Chirality : 0.039 0.138 687 Planarity : 0.004 0.044 749 Dihedral : 5.091 58.914 590 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.26 % Allowed : 21.09 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.37), residues: 539 helix: 1.69 (0.27), residues: 380 sheet: None (None), residues: 0 loop : 0.19 (0.52), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 587 TYR 0.019 0.001 TYR A 84 PHE 0.018 0.001 PHE A 408 TRP 0.006 0.001 TRP A 128 HIS 0.003 0.001 HIS A 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.13 ( 4530) covalent geometry : angle 0.52879 / 0.26 ( 6178) SS BOND : bond 0.00237 / 0.15 ( 1) SS BOND : angle 0.99051 / 0.46 ( 2) hydrogen bonds : bond 0.03893 / 2.62 ( 289) hydrogen bonds : angle 4.77897 / 3.55 ( 843) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: A 418 ASP cc_start: 0.7614 (OUTLIER) cc_final: 0.7248 (m-30) REVERT: A 507 GLN cc_start: 0.8313 (tt0) cc_final: 0.7802 (tt0) REVERT: A 584 LEU cc_start: 0.6871 (tp) cc_final: 0.6629 (tp) REVERT: A 595 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7485 (mt-10) outliers start: 15 outliers final: 10 residues processed: 65 average time/residue: 0.2480 time to fit residues: 17.3849 Evaluate side-chains 67 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 617 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 18 optimal weight: 0.1980 chunk 36 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 11 optimal weight: 0.0970 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 47 optimal weight: 0.4980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.143712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.121431 restraints weight = 4834.323| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.22 r_work: 0.3189 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.7572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4531 Z= 0.120 Angle : 0.515 7.147 6180 Z= 0.257 Chirality : 0.038 0.135 687 Planarity : 0.004 0.043 749 Dihedral : 4.987 54.373 590 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.70 % Allowed : 21.30 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.37), residues: 539 helix: 1.77 (0.27), residues: 379 sheet: None (None), residues: 0 loop : 0.23 (0.52), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 121 TYR 0.018 0.001 TYR A 84 PHE 0.049 0.001 PHE A 408 TRP 0.006 0.001 TRP A 235 HIS 0.003 0.001 HIS A 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 4530) covalent geometry : angle 0.51447 / 0.26 ( 6178) SS BOND : bond 0.00159 / 0.10 ( 1) SS BOND : angle 0.85333 / 0.40 ( 2) hydrogen bonds : bond 0.03762 / 2.53 ( 289) hydrogen bonds : angle 4.70967 / 3.50 ( 843) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.194 Fit side-chains REVERT: A 373 LYS cc_start: 0.8414 (mmmm) cc_final: 0.7904 (mtmt) REVERT: A 403 PHE cc_start: 0.8126 (t80) cc_final: 0.7739 (t80) REVERT: A 418 ASP cc_start: 0.7570 (OUTLIER) cc_final: 0.7185 (m-30) REVERT: A 507 GLN cc_start: 0.8326 (tt0) cc_final: 0.7887 (tt0) REVERT: A 584 LEU cc_start: 0.6872 (tp) cc_final: 0.6622 (tp) REVERT: A 595 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7464 (mt-10) outliers start: 17 outliers final: 9 residues processed: 72 average time/residue: 0.2662 time to fit residues: 20.6619 Evaluate side-chains 72 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 617 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 32 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 0.0970 chunk 39 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 181 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 = 0.3516 r_free = 0.3516 target = 0.143559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.121184 restraints weight = 4838.381| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.23 r_work: 0.3180 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.7632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4531 Z= 0.127 Angle : 0.528 7.209 6180 Z= 0.265 Chirality : 0.039 0.165 687 Planarity : 0.004 0.042 749 Dihedral : 4.902 49.930 590 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.48 % Allowed : 21.09 % Favored : 75.43 % 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 are not related in a simple way. whole: 1.89 (0.37), residues: 539 helix: 1.71 (0.27), residues: 379 sheet: None (None), residues: 0 loop : 0.29 (0.52), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 121 TYR 0.019 0.001 TYR A 84 PHE 0.047 0.001 PHE A 408 TRP 0.006 0.001 TRP A 128 HIS 0.003 0.001 HIS A 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 4530) covalent geometry : angle 0.52747 / 0.26 ( 6178) SS BOND : bond 0.00248 / 0.16 ( 1) SS BOND : angle 0.99560 / 0.46 ( 2) hydrogen bonds : bond 0.03822 / 2.58 ( 289) hydrogen bonds : angle 4.75025 / 3.56 ( 843) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.115 Fit side-chains REVERT: A 373 LYS cc_start: 0.8432 (mmmm) cc_final: 0.7886 (mtmt) REVERT: A 403 PHE cc_start: 0.8119 (t80) cc_final: 0.7770 (t80) REVERT: A 418 ASP cc_start: 0.7577 (OUTLIER) cc_final: 0.7186 (m-30) REVERT: A 507 GLN cc_start: 0.8327 (tt0) cc_final: 0.7885 (tt0) REVERT: A 595 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7465 (mt-10) outliers start: 16 outliers final: 10 residues processed: 70 average time/residue: 0.2834 time to fit residues: 21.3031 Evaluate side-chains 72 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 617 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 12 optimal weight: 0.1980 chunk 3 optimal weight: 0.9990 chunk 8 optimal weight: 0.4980 chunk 43 optimal weight: 0.6980 chunk 47 optimal weight: 0.0770 chunk 40 optimal weight: 1.9990 chunk 17 optimal weight: 0.0870 chunk 42 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 overall best weight: 0.2916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 181 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 = 0.3683 r_free = 0.3683 target = 0.153930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.129054 restraints weight = 4576.389| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.46 r_work: 0.3291 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.7662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4531 Z= 0.108 Angle : 0.507 6.769 6180 Z= 0.251 Chirality : 0.038 0.201 687 Planarity : 0.004 0.044 749 Dihedral : 4.791 48.811 590 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.96 % Allowed : 22.61 % Favored : 75.43 % 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 are not related in a simple way. whole: 2.05 (0.37), residues: 539 helix: 1.79 (0.27), residues: 380 sheet: None (None), residues: 0 loop : 0.46 (0.53), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 121 TYR 0.016 0.001 TYR A 84 PHE 0.042 0.001 PHE A 408 TRP 0.006 0.001 TRP A 235 HIS 0.003 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 4530) covalent geometry : angle 0.50722 / 0.25 ( 6178) SS BOND : bond 0.00143 / 0.09 ( 1) SS BOND : angle 0.84369 / 0.39 ( 2) hydrogen bonds : bond 0.03608 / 2.44 ( 289) hydrogen bonds : angle 4.62853 / 3.45 ( 843) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.159 Fit side-chains REVERT: A 107 MET cc_start: 0.8765 (ttt) cc_final: 0.8387 (tmm) REVERT: A 373 LYS cc_start: 0.8248 (mmmm) cc_final: 0.7623 (mtmt) REVERT: A 403 PHE cc_start: 0.7883 (t80) cc_final: 0.7486 (t80) REVERT: A 418 ASP cc_start: 0.7368 (OUTLIER) cc_final: 0.6843 (m-30) REVERT: A 507 GLN cc_start: 0.8143 (tt0) cc_final: 0.7719 (tt0) REVERT: A 556 TRP cc_start: 0.7902 (m100) cc_final: 0.6490 (m-10) outliers start: 9 outliers final: 5 residues processed: 68 average time/residue: 0.2771 time to fit residues: 20.3167 Evaluate side-chains 67 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 617 ILE 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 29 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 12 optimal weight: 0.0870 chunk 44 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 181 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 = 0.3530 r_free = 0.3530 target = 0.144317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.122569 restraints weight = 4757.117| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.22 r_work: 0.3177 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.7692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4531 Z= 0.132 Angle : 0.539 7.061 6180 Z= 0.269 Chirality : 0.040 0.220 687 Planarity : 0.004 0.042 749 Dihedral : 4.654 46.662 590 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.74 % Allowed : 23.70 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.37), residues: 539 helix: 1.73 (0.27), residues: 380 sheet: None (None), residues: 0 loop : 0.49 (0.53), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 121 TYR 0.020 0.001 TYR A 391 PHE 0.046 0.001 PHE A 408 TRP 0.006 0.001 TRP A 128 HIS 0.003 0.001 HIS A 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 ( 4530) covalent geometry : angle 0.53906 / 0.27 ( 6178) SS BOND : bond 0.00219 / 0.14 ( 1) SS BOND : angle 0.92975 / 0.43 ( 2) hydrogen bonds : bond 0.03885 / 2.65 ( 289) hydrogen bonds : angle 4.72758 / 3.55 ( 843) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.162 Fit side-chains REVERT: A 174 THR cc_start: 0.8533 (m) cc_final: 0.8083 (p) REVERT: A 373 LYS cc_start: 0.8427 (mmmm) cc_final: 0.7905 (mtmt) REVERT: A 403 PHE cc_start: 0.8136 (t80) cc_final: 0.7847 (t80) REVERT: A 418 ASP cc_start: 0.7554 (OUTLIER) cc_final: 0.7174 (m-30) REVERT: A 507 GLN cc_start: 0.8313 (tt0) cc_final: 0.7939 (tt0) outliers start: 8 outliers final: 5 residues processed: 65 average time/residue: 0.2716 time to fit residues: 19.0111 Evaluate side-chains 67 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 617 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 39 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 9 optimal weight: 0.4980 chunk 14 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 0.1980 chunk 27 optimal weight: 2.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 181 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 = 0.3674 r_free = 0.3674 target = 0.152933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.128013 restraints weight = 4643.419| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.46 r_work: 0.3278 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.7763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 4531 Z= 0.126 Angle : 0.538 7.766 6180 Z= 0.269 Chirality : 0.040 0.207 687 Planarity : 0.004 0.041 749 Dihedral : 4.538 47.977 590 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.52 % Allowed : 24.13 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.37), residues: 539 helix: 1.70 (0.27), residues: 380 sheet: None (None), residues: 0 loop : 0.58 (0.53), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 121 TYR 0.018 0.001 TYR A 391 PHE 0.045 0.001 PHE A 408 TRP 0.005 0.001 TRP A 128 HIS 0.003 0.001 HIS A 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 4530) covalent geometry : angle 0.53833 / 0.27 ( 6178) SS BOND : bond 0.00184 / 0.11 ( 1) SS BOND : angle 0.89208 / 0.42 ( 2) hydrogen bonds : bond 0.03837 / 2.62 ( 289) hydrogen bonds : angle 4.73783 / 3.58 ( 843) =============================================================================== Job complete usr+sys time: 1383.54 seconds wall clock time: 24 minutes 20.26 seconds (1460.26 seconds total)