Starting phenix.real_space_refine on Fri Aug 22 14:46:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hfg_34720/08_2025/8hfg_34720.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hfg_34720/08_2025/8hfg_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hfg_34720/08_2025/8hfg_34720.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hfg_34720/08_2025/8hfg_34720.map" model { file = "/net/cci-nas-00/data/ceres_data/8hfg_34720/08_2025/8hfg_34720.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hfg_34720/08_2025/8hfg_34720.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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-2.0-5787/lib/python3.9/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, 28 Unusual residues: {' CL': 1, 'LDP': 2} Classifications: {'undetermined': 3, 'water': 5} Link IDs: {None: 7} Time building chain proxies: 1.02, per 1000 atoms: 0.23 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: 0.43 Conformation dependent library (CDL) restraints added in 165.2 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.15 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: 0.50 Time building geometry restraints manager: 0.53 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: 0.420 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: 0.020 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.380 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:5.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 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 aren 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 covalent geometry : bond 0.00611 ( 4530) covalent geometry : angle 0.80407 ( 6178) SS BOND : bond 0.00181 ( 1) SS BOND : angle 1.24496 ( 2) hydrogen bonds : bond 0.11866 ( 289) hydrogen bonds : angle 5.11628 ( 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 : 0.137 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: 0.3477 time to fit residues: 31.4565 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 : 0.090 ------------------------------------------------------------------------------- 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: 0.0870 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 19 optimal weight: 0.1980 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3664 r_free = 0.3664 target = 0.159610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.133658 restraints weight = 4829.703| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.53 r_work: 0.3302 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4531 Z= 0.154 Angle : 0.562 6.889 6180 Z= 0.292 Chirality : 0.040 0.144 687 Planarity : 0.005 0.062 749 Dihedral : 5.920 77.982 595 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.70 % Allowed : 17.17 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.85 (0.38), residues: 539 helix: 1.75 (0.27), residues: 378 sheet: None (None), residues: 0 loop : 0.09 (0.53), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 301 TYR 0.014 0.002 TYR A 205 PHE 0.023 0.001 PHE A 408 TRP 0.022 0.001 TRP A 235 HIS 0.004 0.001 HIS A 599 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 4530) covalent geometry : angle 0.56144 ( 6178) SS BOND : bond 0.01810 ( 1) SS BOND : angle 1.12155 ( 2) hydrogen bonds : bond 0.04085 ( 289) hydrogen bonds : angle 4.63348 ( 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 90 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.143 Fit side-chains REVERT: A 236 GLN cc_start: 0.7542 (mt0) cc_final: 0.7248 (mp10) REVERT: A 310 ASP cc_start: 0.7623 (m-30) cc_final: 0.7363 (t0) REVERT: A 373 LYS cc_start: 0.7610 (mmmm) cc_final: 0.7337 (mmtt) REVERT: A 507 GLN cc_start: 0.7846 (tt0) cc_final: 0.7456 (tt0) REVERT: A 588 LEU cc_start: 0.7230 (OUTLIER) cc_final: 0.6593 (mm) outliers start: 17 outliers final: 3 residues processed: 84 average time/residue: 0.2665 time to fit residues: 23.9807 Evaluate side-chains 65 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 588 LEU 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: 2.9990 chunk 39 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 31 optimal weight: 0.1980 chunk 26 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN A 234 GLN A 372 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.152035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.125361 restraints weight = 4762.857| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.50 r_work: 0.3216 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.6063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4531 Z= 0.146 Angle : 0.580 7.967 6180 Z= 0.290 Chirality : 0.040 0.136 687 Planarity : 0.005 0.055 749 Dihedral : 5.439 66.396 592 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.35 % Allowed : 17.39 % 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 aren not related in a simple way. whole: 1.65 (0.37), residues: 539 helix: 1.52 (0.27), residues: 380 sheet: None (None), residues: 0 loop : 0.21 (0.54), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 512 TYR 0.015 0.002 TYR A 271 PHE 0.018 0.001 PHE A 408 TRP 0.011 0.001 TRP A 235 HIS 0.004 0.001 HIS A 599 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 4530) covalent geometry : angle 0.57907 ( 6178) SS BOND : bond 0.00981 ( 1) SS BOND : angle 2.33297 ( 2) hydrogen bonds : bond 0.04145 ( 289) hydrogen bonds : angle 4.81265 ( 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: 20 poor density : 68 time to evaluate : 0.109 Fit side-chains REVERT: A 109 LEU cc_start: 0.7829 (mm) cc_final: 0.7511 (mt) REVERT: A 204 LYS cc_start: 0.6749 (OUTLIER) cc_final: 0.6398 (tptt) REVERT: A 373 LYS cc_start: 0.7751 (mmmm) cc_final: 0.7285 (mmpt) REVERT: A 375 ASN cc_start: 0.7683 (m-40) cc_final: 0.7291 (t0) REVERT: A 403 PHE cc_start: 0.7686 (t80) cc_final: 0.7375 (t80) REVERT: A 431 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7669 (mt) REVERT: A 500 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.6865 (ttp-170) REVERT: A 507 GLN cc_start: 0.8068 (tt0) cc_final: 0.7569 (tt0) outliers start: 20 outliers final: 3 residues processed: 84 average time/residue: 0.2388 time to fit residues: 21.6288 Evaluate side-chains 69 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.172 ------------------------------------------------------------------------------- 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 431 LEU Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 500 ARG 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: 2.9990 chunk 24 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 0.0470 chunk 53 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.160128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.132712 restraints weight = 4575.276| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.70 r_work: 0.3348 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.6720 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= 0.133 Angle : 0.539 7.884 6180 Z= 0.268 Chirality : 0.040 0.160 687 Planarity : 0.004 0.048 749 Dihedral : 5.304 66.238 590 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.83 % Allowed : 20.43 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.85 (0.37), residues: 539 helix: 1.70 (0.27), residues: 379 sheet: None (None), residues: 0 loop : 0.23 (0.53), residues: 160 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 0.029 0.001 PHE A 408 TRP 0.009 0.001 TRP A 235 HIS 0.004 0.001 HIS A 599 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 4530) covalent geometry : angle 0.53878 ( 6178) SS BOND : bond 0.00033 ( 1) SS BOND : angle 0.95221 ( 2) hydrogen bonds : bond 0.03964 ( 289) hydrogen bonds : angle 4.78052 ( 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 79 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.127 Fit side-chains REVERT: A 189 LYS cc_start: 0.7149 (mtmm) cc_final: 0.6901 (mttp) REVERT: A 204 LYS cc_start: 0.6716 (OUTLIER) cc_final: 0.6496 (tptt) REVERT: A 373 LYS cc_start: 0.7882 (mmmm) cc_final: 0.7412 (mmtm) REVERT: A 500 ARG cc_start: 0.7271 (OUTLIER) cc_final: 0.6831 (ttp-170) REVERT: A 507 GLN cc_start: 0.8171 (tt0) cc_final: 0.7664 (tt0) REVERT: A 556 TRP cc_start: 0.7936 (m100) cc_final: 0.6472 (m-10) outliers start: 13 outliers final: 5 residues processed: 75 average time/residue: 0.2992 time to fit residues: 23.8700 Evaluate side-chains 67 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.140 ------------------------------------------------------------------------------- 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 462 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 500 ARG Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 588 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 11 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.156240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.128338 restraints weight = 4623.037| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.77 r_work: 0.3321 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.7269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4531 Z= 0.158 Angle : 0.560 7.974 6180 Z= 0.279 Chirality : 0.041 0.164 687 Planarity : 0.004 0.045 749 Dihedral : 5.149 59.770 590 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.26 % Allowed : 20.43 % 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 aren not related in a simple way. whole: 1.65 (0.37), residues: 539 helix: 1.55 (0.27), residues: 381 sheet: None (None), residues: 0 loop : 0.10 (0.51), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 518 TYR 0.021 0.001 TYR A 84 PHE 0.039 0.001 PHE A 408 TRP 0.007 0.001 TRP A 128 HIS 0.003 0.001 HIS A 599 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 4530) covalent geometry : angle 0.55997 ( 6178) SS BOND : bond 0.00258 ( 1) SS BOND : angle 1.20677 ( 2) hydrogen bonds : bond 0.04170 ( 289) hydrogen bonds : angle 4.87149 ( 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 75 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.170 Fit side-chains REVERT: A 109 LEU cc_start: 0.7817 (mm) cc_final: 0.7588 (mt) REVERT: A 189 LYS cc_start: 0.7209 (mtmm) cc_final: 0.6994 (mttp) REVERT: A 368 MET cc_start: 0.8284 (mtt) cc_final: 0.7902 (mtp) REVERT: A 373 LYS cc_start: 0.7944 (mmmm) cc_final: 0.7433 (mtmt) REVERT: A 500 ARG cc_start: 0.7242 (OUTLIER) cc_final: 0.6788 (ttp-170) REVERT: A 507 GLN cc_start: 0.8224 (tt0) cc_final: 0.7667 (tt0) outliers start: 15 outliers final: 6 residues processed: 69 average time/residue: 0.3283 time to fit residues: 24.0271 Evaluate side-chains 67 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 500 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 50 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 18 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 25 optimal weight: 0.0970 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.158306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.130656 restraints weight = 4706.257| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.80 r_work: 0.3356 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.7372 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= 0.118 Angle : 0.520 7.638 6180 Z= 0.259 Chirality : 0.038 0.135 687 Planarity : 0.004 0.044 749 Dihedral : 5.029 56.944 590 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.17 % Allowed : 22.61 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.37), residues: 539 helix: 1.66 (0.27), residues: 382 sheet: None (None), residues: 0 loop : 0.19 (0.52), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 121 TYR 0.017 0.001 TYR A 84 PHE 0.034 0.001 PHE A 408 TRP 0.007 0.001 TRP A 235 HIS 0.003 0.001 HIS A 599 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 4530) covalent geometry : angle 0.51951 ( 6178) SS BOND : bond 0.00186 ( 1) SS BOND : angle 0.88051 ( 2) hydrogen bonds : bond 0.03750 ( 289) hydrogen bonds : angle 4.74843 ( 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 73 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.139 Fit side-chains REVERT: A 368 MET cc_start: 0.8297 (mtt) cc_final: 0.8016 (mtp) REVERT: A 373 LYS cc_start: 0.7918 (mmmm) cc_final: 0.7391 (mmtm) REVERT: A 418 ASP cc_start: 0.7436 (OUTLIER) cc_final: 0.6915 (m-30) REVERT: A 500 ARG cc_start: 0.7210 (OUTLIER) cc_final: 0.6744 (ttp-170) REVERT: A 507 GLN cc_start: 0.8180 (tt0) cc_final: 0.7678 (tt0) outliers start: 10 outliers final: 7 residues processed: 68 average time/residue: 0.2985 time to fit residues: 21.5269 Evaluate side-chains 68 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.104 ------------------------------------------------------------------------------- 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 398 LEU 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 500 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 18 optimal weight: 0.2980 chunk 36 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3737 r_free = 0.3737 target = 0.154977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.129400 restraints weight = 4706.680| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.64 r_work: 0.3337 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.7515 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= 0.142 Angle : 0.540 7.088 6180 Z= 0.268 Chirality : 0.040 0.181 687 Planarity : 0.004 0.043 749 Dihedral : 4.918 50.650 590 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.48 % Allowed : 22.39 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.37), residues: 539 helix: 1.64 (0.27), residues: 380 sheet: None (None), residues: 0 loop : 0.12 (0.52), 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 84 PHE 0.059 0.002 PHE A 408 TRP 0.006 0.001 TRP A 128 HIS 0.004 0.001 HIS A 599 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 4530) covalent geometry : angle 0.54023 ( 6178) SS BOND : bond 0.00294 ( 1) SS BOND : angle 0.97862 ( 2) hydrogen bonds : bond 0.03980 ( 289) hydrogen bonds : angle 4.79183 ( 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 78 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.105 Fit side-chains REVERT: A 373 LYS cc_start: 0.8016 (mmmm) cc_final: 0.7526 (mtmt) REVERT: A 403 PHE cc_start: 0.7963 (t80) cc_final: 0.7497 (t80) REVERT: A 418 ASP cc_start: 0.7525 (OUTLIER) cc_final: 0.7032 (m-30) REVERT: A 500 ARG cc_start: 0.7351 (OUTLIER) cc_final: 0.6918 (ttp-170) REVERT: A 507 GLN cc_start: 0.8268 (tt0) cc_final: 0.7744 (tt0) REVERT: A 588 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7256 (mm) outliers start: 16 outliers final: 9 residues processed: 71 average time/residue: 0.2486 time to fit residues: 18.9290 Evaluate side-chains 71 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 127 VAL 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 336 ASP Chi-restraints excluded: chain A residue 398 LEU 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 500 ARG Chi-restraints excluded: chain A residue 588 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 32 optimal weight: 0.0870 chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 0.2980 chunk 39 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.157613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.131939 restraints weight = 4693.880| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.66 r_work: 0.3370 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.7575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4531 Z= 0.120 Angle : 0.535 7.206 6180 Z= 0.264 Chirality : 0.039 0.155 687 Planarity : 0.004 0.044 749 Dihedral : 4.734 44.327 590 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.70 % Allowed : 22.61 % Favored : 73.70 % 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 aren not related in a simple way. whole: 1.84 (0.37), residues: 539 helix: 1.68 (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 0.017 0.001 TYR A 84 PHE 0.048 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 covalent geometry : bond 0.00285 ( 4530) covalent geometry : angle 0.53464 ( 6178) SS BOND : bond 0.00175 ( 1) SS BOND : angle 0.82862 ( 2) hydrogen bonds : bond 0.03769 ( 289) hydrogen bonds : angle 4.73592 ( 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 79 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.150 Fit side-chains REVERT: A 174 THR cc_start: 0.8296 (m) cc_final: 0.7777 (p) REVERT: A 373 LYS cc_start: 0.7972 (mmmm) cc_final: 0.7493 (mtmt) REVERT: A 403 PHE cc_start: 0.7893 (t80) cc_final: 0.7433 (t80) REVERT: A 418 ASP cc_start: 0.7456 (OUTLIER) cc_final: 0.6948 (m-30) REVERT: A 500 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.6878 (ttp-170) REVERT: A 507 GLN cc_start: 0.8189 (tt0) cc_final: 0.7701 (tt0) REVERT: A 556 TRP cc_start: 0.7934 (m100) cc_final: 0.6504 (m-10) REVERT: A 588 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7327 (mm) outliers start: 17 outliers final: 8 residues processed: 71 average time/residue: 0.2604 time to fit residues: 19.7967 Evaluate side-chains 70 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 398 LEU 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 500 ARG Chi-restraints excluded: chain A residue 588 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 12 optimal weight: 0.0570 chunk 3 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 17 optimal weight: 0.0970 chunk 42 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.145238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.122849 restraints weight = 4814.326| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.23 r_work: 0.3199 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.7657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4531 Z= 0.115 Angle : 0.524 6.801 6180 Z= 0.258 Chirality : 0.038 0.198 687 Planarity : 0.004 0.044 749 Dihedral : 4.491 45.891 590 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.39 % Allowed : 23.04 % 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 aren not related in a simple way. whole: 1.91 (0.37), residues: 539 helix: 1.73 (0.27), residues: 379 sheet: None (None), residues: 0 loop : 0.28 (0.52), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 121 TYR 0.017 0.001 TYR A 84 PHE 0.044 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 covalent geometry : bond 0.00270 ( 4530) covalent geometry : angle 0.52406 ( 6178) SS BOND : bond 0.00169 ( 1) SS BOND : angle 0.73818 ( 2) hydrogen bonds : bond 0.03671 ( 289) hydrogen bonds : angle 4.67472 ( 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 78 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.102 Fit side-chains REVERT: A 107 MET cc_start: 0.8856 (ttt) cc_final: 0.8614 (tmm) REVERT: A 174 THR cc_start: 0.8500 (m) cc_final: 0.8058 (p) REVERT: A 373 LYS cc_start: 0.8248 (mmmm) cc_final: 0.7899 (mtmt) REVERT: A 403 PHE cc_start: 0.8109 (t80) cc_final: 0.7733 (t80) REVERT: A 418 ASP cc_start: 0.7524 (OUTLIER) cc_final: 0.7120 (m-30) REVERT: A 500 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.7217 (ttp-170) REVERT: A 507 GLN cc_start: 0.8319 (tt0) cc_final: 0.7896 (tt0) REVERT: A 588 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7419 (mm) outliers start: 11 outliers final: 7 residues processed: 72 average time/residue: 0.2736 time to fit residues: 21.1717 Evaluate side-chains 74 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 500 ARG Chi-restraints excluded: chain A residue 588 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 33 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 12 optimal weight: 0.0970 chunk 44 optimal weight: 0.6980 chunk 19 optimal weight: 0.4980 chunk 26 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.144421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.122023 restraints weight = 4859.817| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.24 r_work: 0.3177 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.7695 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= 0.125 Angle : 0.543 7.199 6180 Z= 0.266 Chirality : 0.039 0.197 687 Planarity : 0.004 0.043 749 Dihedral : 4.506 45.024 590 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.61 % Allowed : 23.26 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.88 (0.37), residues: 539 helix: 1.69 (0.27), residues: 380 sheet: None (None), residues: 0 loop : 0.31 (0.52), 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 84 PHE 0.044 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 covalent geometry : bond 0.00300 ( 4530) covalent geometry : angle 0.54256 ( 6178) SS BOND : bond 0.00221 ( 1) SS BOND : angle 0.79104 ( 2) hydrogen bonds : bond 0.03798 ( 289) hydrogen bonds : angle 4.70953 ( 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 76 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.177 Fit side-chains REVERT: A 107 MET cc_start: 0.8922 (ttt) cc_final: 0.8652 (tmm) REVERT: A 174 THR cc_start: 0.8529 (m) cc_final: 0.8094 (p) REVERT: A 373 LYS cc_start: 0.8329 (mmmm) cc_final: 0.7915 (mtmt) REVERT: A 403 PHE cc_start: 0.8112 (t80) cc_final: 0.7745 (t80) REVERT: A 418 ASP cc_start: 0.7516 (OUTLIER) cc_final: 0.7128 (m-30) REVERT: A 500 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.7235 (ttp-170) REVERT: A 507 GLN cc_start: 0.8326 (tt0) cc_final: 0.7887 (tt0) REVERT: A 556 TRP cc_start: 0.8061 (m100) cc_final: 0.6882 (m-10) REVERT: A 588 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7488 (mm) outliers start: 12 outliers final: 7 residues processed: 70 average time/residue: 0.3215 time to fit residues: 23.8465 Evaluate side-chains 72 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 500 ARG Chi-restraints excluded: chain A residue 588 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 39 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.142717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.120299 restraints weight = 4871.104| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.24 r_work: 0.3159 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.7747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4531 Z= 0.135 Angle : 0.558 8.116 6180 Z= 0.273 Chirality : 0.039 0.197 687 Planarity : 0.004 0.043 749 Dihedral : 4.511 43.585 590 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.39 % Allowed : 23.91 % Favored : 73.70 % 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 aren not related in a simple way. whole: 1.80 (0.37), residues: 539 helix: 1.62 (0.27), residues: 380 sheet: None (None), residues: 0 loop : 0.32 (0.52), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 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 covalent geometry : bond 0.00327 ( 4530) covalent geometry : angle 0.55756 ( 6178) SS BOND : bond 0.00245 ( 1) SS BOND : angle 0.90017 ( 2) hydrogen bonds : bond 0.03909 ( 289) hydrogen bonds : angle 4.75635 ( 843) =============================================================================== Job complete usr+sys time: 1379.11 seconds wall clock time: 24 minutes 14.73 seconds (1454.73 seconds total)