Starting phenix.real_space_refine on Sat May 10 21:01:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ubz_42110/05_2025/8ubz_42110_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ubz_42110/05_2025/8ubz_42110.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ubz_42110/05_2025/8ubz_42110.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ubz_42110/05_2025/8ubz_42110.map" model { file = "/net/cci-nas-00/data/ceres_data/8ubz_42110/05_2025/8ubz_42110_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ubz_42110/05_2025/8ubz_42110_trim.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.027 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 18 5.16 5 C 2243 2.51 5 N 496 2.21 5 O 602 1.98 5 H 3315 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6674 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 6536 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 17, 'TRANS': 397} Chain: "A" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 138 Unusual residues: {'CHT': 1, 'Y01': 3} Classifications: {'undetermined': 4, 'water': 26} Link IDs: {None: 29} Time building chain proxies: 4.31, per 1000 atoms: 0.65 Number of scatterers: 6674 At special positions: 0 Unit cell: (84.252, 56.994, 66.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 O 602 8.00 N 496 7.00 C 2243 6.00 H 3315 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 536.5 milliseconds 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 0 sheets defined 90.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 105 through 131 removed outlier: 3.886A pdb=" N VAL A 109 " --> pdb=" O PRO A 105 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN A 121 " --> pdb=" O TYR A 117 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N TYR A 128 " --> pdb=" O GLN A 124 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N SER A 129 " --> pdb=" O TRP A 125 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE A 131 " --> pdb=" O GLN A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 140 Processing helix chain 'A' and resid 142 through 171 removed outlier: 3.913A pdb=" N ILE A 146 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N TYR A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N MET A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) Proline residue: A 159 - end of helix removed outlier: 5.616A pdb=" N PHE A 162 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Proline residue: A 163 - end of helix Processing helix chain 'A' and resid 172 through 193 removed outlier: 3.697A pdb=" N THR A 176 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY A 193 " --> pdb=" O TRP A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 219 removed outlier: 3.712A pdb=" N THR A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE A 216 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLY A 219 " --> pdb=" O VAL A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 229 removed outlier: 4.367A pdb=" N ARG A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 260 Proline residue: A 256 - end of helix Processing helix chain 'A' and resid 266 through 296 removed outlier: 3.670A pdb=" N LEU A 270 " --> pdb=" O ASP A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 314 Processing helix chain 'A' and resid 320 through 331 removed outlier: 3.859A pdb=" N ASN A 331 " --> pdb=" O ASN A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 363 removed outlier: 5.074A pdb=" N ASN A 356 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N GLN A 357 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR A 362 " --> pdb=" O MET A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 396 Processing helix chain 'A' and resid 399 through 420 Processing helix chain 'A' and resid 421 through 423 No H-bonds generated for 'chain 'A' and resid 421 through 423' Processing helix chain 'A' and resid 424 through 454 removed outlier: 3.505A pdb=" N LEU A 443 " --> pdb=" O MET A 439 " (cutoff:3.500A) Proline residue: A 444 - end of helix Processing helix chain 'A' and resid 458 through 489 Processing helix chain 'A' and resid 489 through 511 removed outlier: 3.900A pdb=" N GLY A 493 " --> pdb=" O GLY A 489 " (cutoff:3.500A) 275 hydrogen bonds defined for protein. 825 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: 2.32 Time building geometry restraints manager: 2.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3307 1.03 - 1.23: 11 1.23 - 1.42: 1383 1.42 - 1.61: 2010 1.61 - 1.81: 28 Bond restraints: 6739 Sorted by residual: bond pdb=" CB PRO A 231 " pdb=" CG PRO A 231 " ideal model delta sigma weight residual 1.492 1.558 -0.066 5.00e-02 4.00e+02 1.75e+00 bond pdb=" CA LEU A 220 " pdb=" C LEU A 220 " ideal model delta sigma weight residual 1.522 1.530 -0.008 1.26e-02 6.30e+03 4.31e-01 bond pdb=" CB PRO A 257 " pdb=" CG PRO A 257 " ideal model delta sigma weight residual 1.492 1.523 -0.031 5.00e-02 4.00e+02 3.89e-01 bond pdb=" CG GLN A 197 " pdb=" CD GLN A 197 " ideal model delta sigma weight residual 1.516 1.531 -0.015 2.50e-02 1.60e+03 3.77e-01 bond pdb=" C LEU A 220 " pdb=" O LEU A 220 " ideal model delta sigma weight residual 1.244 1.238 0.006 9.80e-03 1.04e+04 3.42e-01 ... (remaining 6734 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 12036 1.68 - 3.36: 119 3.36 - 5.04: 13 5.04 - 6.73: 2 6.73 - 8.41: 1 Bond angle restraints: 12171 Sorted by residual: angle pdb=" C GLY A 219 " pdb=" N LEU A 220 " pdb=" CA LEU A 220 " ideal model delta sigma weight residual 120.09 123.77 -3.68 1.25e+00 6.40e-01 8.66e+00 angle pdb=" CB PRO A 159 " pdb=" CG PRO A 159 " pdb=" CD PRO A 159 " ideal model delta sigma weight residual 106.10 97.69 8.41 3.20e+00 9.77e-02 6.90e+00 angle pdb=" CA PRO A 159 " pdb=" CB PRO A 159 " pdb=" CG PRO A 159 " ideal model delta sigma weight residual 104.50 99.61 4.89 1.90e+00 2.77e-01 6.61e+00 angle pdb=" CA PRO A 159 " pdb=" N PRO A 159 " pdb=" CD PRO A 159 " ideal model delta sigma weight residual 112.00 108.68 3.32 1.40e+00 5.10e-01 5.64e+00 angle pdb=" N PRO A 159 " pdb=" CA PRO A 159 " pdb=" CB PRO A 159 " ideal model delta sigma weight residual 103.46 101.38 2.08 9.30e-01 1.16e+00 5.01e+00 ... (remaining 12166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 2960 17.40 - 34.80: 239 34.80 - 52.20: 90 52.20 - 69.60: 50 69.60 - 87.00: 3 Dihedral angle restraints: 3342 sinusoidal: 1874 harmonic: 1468 Sorted by residual: dihedral pdb=" CA TYR A 117 " pdb=" C TYR A 117 " pdb=" N SER A 118 " pdb=" CA SER A 118 " ideal model delta harmonic sigma weight residual 180.00 162.53 17.47 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CB MET A 413 " pdb=" CG MET A 413 " pdb=" SD MET A 413 " pdb=" CE MET A 413 " ideal model delta sinusoidal sigma weight residual -180.00 -120.85 -59.15 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB LYS A 491 " pdb=" CG LYS A 491 " pdb=" CD LYS A 491 " pdb=" CE LYS A 491 " ideal model delta sinusoidal sigma weight residual -180.00 -122.51 -57.49 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 3339 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 426 0.029 - 0.058: 68 0.058 - 0.087: 58 0.087 - 0.115: 11 0.115 - 0.144: 1 Chirality restraints: 564 Sorted by residual: chirality pdb=" CA PRO A 231 " pdb=" N PRO A 231 " pdb=" C PRO A 231 " pdb=" CB PRO A 231 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA PRO A 221 " pdb=" N PRO A 221 " pdb=" C PRO A 221 " pdb=" CB PRO A 221 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.61e-01 chirality pdb=" CA TYR A 117 " pdb=" N TYR A 117 " pdb=" C TYR A 117 " pdb=" CB TYR A 117 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.10 2.00e-01 2.50e+01 2.40e-01 ... (remaining 561 not shown) Planarity restraints: 949 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 256 " 0.052 5.00e-02 4.00e+02 7.81e-02 9.77e+00 pdb=" N PRO A 257 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 257 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 257 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 230 " -0.051 5.00e-02 4.00e+02 7.57e-02 9.17e+00 pdb=" N PRO A 231 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 231 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 231 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 158 " 0.040 5.00e-02 4.00e+02 5.99e-02 5.74e+00 pdb=" N PRO A 159 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 159 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 159 " 0.033 5.00e-02 4.00e+02 ... (remaining 946 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 815 2.26 - 2.84: 15343 2.84 - 3.43: 18619 3.43 - 4.01: 24731 4.01 - 4.60: 38275 Nonbonded interactions: 97783 Sorted by model distance: nonbonded pdb="HD22 ASN A 133 " pdb=" OE2 GLU A 367 " model vdw 1.669 2.450 nonbonded pdb=" O ALA A 450 " pdb=" HG1 THR A 454 " model vdw 1.728 2.450 nonbonded pdb=" O SER A 282 " pdb=" HG1 THR A 286 " model vdw 1.731 2.450 nonbonded pdb=" O ASN A 467 " pdb="HE21 GLN A 471 " model vdw 1.798 2.450 nonbonded pdb=" O LYS A 191 " pdb=" HG SER A 194 " model vdw 1.840 2.450 ... (remaining 97778 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: 4.300 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: 0.120 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.800 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:3.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 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 : 0.002 0.066 3424 Z= 0.102 Angle : 0.482 8.408 4688 Z= 0.254 Chirality : 0.033 0.144 564 Planarity : 0.006 0.078 552 Dihedral : 15.414 87.005 1357 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.28 % Allowed : 18.52 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.77 (0.43), residues: 413 helix: 3.14 (0.28), residues: 341 sheet: None (None), residues: 0 loop : -1.00 (0.74), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 391 HIS 0.000 0.000 HIS A 145 PHE 0.010 0.001 PHE A 496 TYR 0.016 0.001 TYR A 117 ARG 0.001 0.000 ARG A 372 Details of bonding type rmsd hydrogen bonds : bond 0.11289 ( 275) hydrogen bonds : angle 5.56429 ( 825) covalent geometry : bond 0.00227 ( 3424) covalent geometry : angle 0.48175 ( 4688) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 GLU cc_start: 0.8182 (tp30) cc_final: 0.7910 (tt0) outliers start: 1 outliers final: 0 residues processed: 90 average time/residue: 0.2898 time to fit residues: 32.2753 Evaluate side-chains 54 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.2980 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 0.3980 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 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 312 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.122344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.105237 restraints weight = 17730.764| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.40 r_work: 0.3366 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3424 Z= 0.154 Angle : 0.518 5.165 4688 Z= 0.277 Chirality : 0.035 0.128 564 Planarity : 0.005 0.055 552 Dihedral : 5.271 56.787 658 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.56 % Allowed : 18.80 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.60 (0.41), residues: 413 helix: 3.07 (0.27), residues: 345 sheet: None (None), residues: 0 loop : -1.62 (0.66), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 391 HIS 0.002 0.001 HIS A 145 PHE 0.012 0.001 PHE A 496 TYR 0.021 0.001 TYR A 117 ARG 0.002 0.000 ARG A 326 Details of bonding type rmsd hydrogen bonds : bond 0.04712 ( 275) hydrogen bonds : angle 4.20073 ( 825) covalent geometry : bond 0.00335 ( 3424) covalent geometry : angle 0.51846 ( 4688) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.466 Fit side-chains revert: symmetry clash REVERT: A 106 ARG cc_start: 0.7914 (ttm-80) cc_final: 0.7309 (ttp-110) REVERT: A 298 GLU cc_start: 0.8568 (tp30) cc_final: 0.7916 (tt0) REVERT: A 452 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7813 (tm-30) outliers start: 9 outliers final: 4 residues processed: 65 average time/residue: 0.2726 time to fit residues: 22.5013 Evaluate side-chains 53 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 469 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 33 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 40 optimal weight: 0.2980 chunk 28 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 13 optimal weight: 0.0870 chunk 34 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.120800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.103460 restraints weight = 17681.373| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.39 r_work: 0.3343 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3424 Z= 0.136 Angle : 0.493 4.875 4688 Z= 0.263 Chirality : 0.035 0.152 564 Planarity : 0.004 0.047 552 Dihedral : 5.049 49.540 658 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.71 % Allowed : 19.09 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.58 (0.41), residues: 413 helix: 3.05 (0.27), residues: 345 sheet: None (None), residues: 0 loop : -1.64 (0.65), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 500 HIS 0.002 0.001 HIS A 145 PHE 0.011 0.001 PHE A 496 TYR 0.020 0.001 TYR A 117 ARG 0.001 0.000 ARG A 326 Details of bonding type rmsd hydrogen bonds : bond 0.04551 ( 275) hydrogen bonds : angle 4.09313 ( 825) covalent geometry : bond 0.00294 ( 3424) covalent geometry : angle 0.49303 ( 4688) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 367 GLU cc_start: 0.8026 (mp0) cc_final: 0.7518 (mp0) REVERT: A 388 CYS cc_start: 0.8725 (m) cc_final: 0.8279 (m) outliers start: 6 outliers final: 4 residues processed: 60 average time/residue: 0.2859 time to fit residues: 21.6299 Evaluate side-chains 59 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 469 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.0670 chunk 0 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 23 optimal weight: 0.0970 chunk 24 optimal weight: 0.9980 chunk 37 optimal weight: 0.3980 chunk 39 optimal weight: 1.9990 chunk 6 optimal weight: 0.0870 chunk 30 optimal weight: 0.9980 overall best weight: 0.3294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.121293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.103968 restraints weight = 17804.943| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.41 r_work: 0.3348 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3424 Z= 0.115 Angle : 0.469 4.671 4688 Z= 0.250 Chirality : 0.034 0.159 564 Planarity : 0.004 0.044 552 Dihedral : 4.826 43.958 658 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.42 % Allowed : 20.23 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.61 (0.42), residues: 413 helix: 3.06 (0.27), residues: 347 sheet: None (None), residues: 0 loop : -1.67 (0.70), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 500 HIS 0.001 0.001 HIS A 145 PHE 0.010 0.001 PHE A 496 TYR 0.019 0.001 TYR A 117 ARG 0.006 0.001 ARG A 301 Details of bonding type rmsd hydrogen bonds : bond 0.04257 ( 275) hydrogen bonds : angle 3.96700 ( 825) covalent geometry : bond 0.00240 ( 3424) covalent geometry : angle 0.46871 ( 4688) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 GLU cc_start: 0.8526 (tp30) cc_final: 0.7791 (tt0) REVERT: A 388 CYS cc_start: 0.8692 (m) cc_final: 0.8250 (m) REVERT: A 457 GLU cc_start: 0.7490 (tp30) cc_final: 0.7270 (tp30) outliers start: 5 outliers final: 1 residues processed: 62 average time/residue: 0.2836 time to fit residues: 22.2407 Evaluate side-chains 55 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 54 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 39 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.116035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.099095 restraints weight = 18130.533| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.39 r_work: 0.3275 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3424 Z= 0.183 Angle : 0.537 5.394 4688 Z= 0.286 Chirality : 0.037 0.196 564 Planarity : 0.004 0.041 552 Dihedral : 5.090 41.553 658 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.71 % Allowed : 19.94 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.24 (0.41), residues: 413 helix: 2.83 (0.27), residues: 345 sheet: None (None), residues: 0 loop : -1.80 (0.62), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 391 HIS 0.002 0.001 HIS A 145 PHE 0.013 0.001 PHE A 496 TYR 0.020 0.001 TYR A 117 ARG 0.001 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.04962 ( 275) hydrogen bonds : angle 4.13601 ( 825) covalent geometry : bond 0.00414 ( 3424) covalent geometry : angle 0.53657 ( 4688) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 CYS cc_start: 0.8686 (m) cc_final: 0.8281 (m) outliers start: 6 outliers final: 6 residues processed: 59 average time/residue: 0.3024 time to fit residues: 22.4931 Evaluate side-chains 59 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 406 TYR Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 510 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 2 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 6 optimal weight: 0.0980 chunk 21 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3632 r_free = 0.3632 target = 0.116543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.099614 restraints weight = 18077.457| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.38 r_work: 0.3279 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3424 Z= 0.146 Angle : 0.495 5.510 4688 Z= 0.265 Chirality : 0.035 0.122 564 Planarity : 0.004 0.042 552 Dihedral : 4.921 41.175 658 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.42 % Allowed : 21.08 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.32 (0.41), residues: 413 helix: 2.89 (0.27), residues: 345 sheet: None (None), residues: 0 loop : -1.77 (0.63), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 500 HIS 0.001 0.001 HIS A 145 PHE 0.011 0.001 PHE A 496 TYR 0.018 0.001 TYR A 117 ARG 0.001 0.000 ARG A 301 Details of bonding type rmsd hydrogen bonds : bond 0.04712 ( 275) hydrogen bonds : angle 4.06220 ( 825) covalent geometry : bond 0.00322 ( 3424) covalent geometry : angle 0.49484 ( 4688) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 367 GLU cc_start: 0.8089 (mp0) cc_final: 0.7572 (mp0) REVERT: A 388 CYS cc_start: 0.8677 (m) cc_final: 0.8279 (m) outliers start: 5 outliers final: 3 residues processed: 62 average time/residue: 0.2784 time to fit residues: 21.7822 Evaluate side-chains 59 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 166 TRP Chi-restraints excluded: chain A residue 291 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 21 optimal weight: 0.1980 chunk 13 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3632 r_free = 0.3632 target = 0.117215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.099927 restraints weight = 17892.289| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.41 r_work: 0.3274 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3424 Z= 0.131 Angle : 0.495 5.098 4688 Z= 0.263 Chirality : 0.035 0.139 564 Planarity : 0.004 0.041 552 Dihedral : 4.735 40.504 658 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.71 % Allowed : 20.51 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.36 (0.41), residues: 413 helix: 2.89 (0.27), residues: 346 sheet: None (None), residues: 0 loop : -1.69 (0.64), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 500 HIS 0.001 0.000 HIS A 145 PHE 0.010 0.001 PHE A 496 TYR 0.019 0.001 TYR A 117 ARG 0.002 0.000 ARG A 301 Details of bonding type rmsd hydrogen bonds : bond 0.04557 ( 275) hydrogen bonds : angle 3.99073 ( 825) covalent geometry : bond 0.00281 ( 3424) covalent geometry : angle 0.49470 ( 4688) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 CYS cc_start: 0.8674 (m) cc_final: 0.8257 (m) outliers start: 6 outliers final: 5 residues processed: 60 average time/residue: 0.2919 time to fit residues: 21.9393 Evaluate side-chains 60 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 406 TYR Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 510 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 0.0870 chunk 33 optimal weight: 0.3980 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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 = 0.3615 r_free = 0.3615 target = 0.115967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.098974 restraints weight = 18100.426| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.39 r_work: 0.3256 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3424 Z= 0.154 Angle : 0.513 4.943 4688 Z= 0.274 Chirality : 0.035 0.130 564 Planarity : 0.005 0.052 552 Dihedral : 4.835 40.455 658 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.85 % Allowed : 19.66 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.24 (0.41), residues: 413 helix: 2.85 (0.27), residues: 345 sheet: None (None), residues: 0 loop : -1.90 (0.63), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 500 HIS 0.001 0.001 HIS A 145 PHE 0.011 0.001 PHE A 496 TYR 0.019 0.001 TYR A 117 ARG 0.009 0.001 ARG A 301 Details of bonding type rmsd hydrogen bonds : bond 0.04695 ( 275) hydrogen bonds : angle 4.03996 ( 825) covalent geometry : bond 0.00344 ( 3424) covalent geometry : angle 0.51261 ( 4688) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 ARG cc_start: 0.8034 (ttm170) cc_final: 0.7775 (ttm110) REVERT: A 388 CYS cc_start: 0.8703 (m) cc_final: 0.8289 (m) outliers start: 10 outliers final: 7 residues processed: 64 average time/residue: 0.3601 time to fit residues: 28.8605 Evaluate side-chains 66 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 406 TYR Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 510 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 2 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 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 = 0.3604 r_free = 0.3604 target = 0.115135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.098006 restraints weight = 18197.346| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.40 r_work: 0.3242 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3424 Z= 0.168 Angle : 0.526 4.854 4688 Z= 0.282 Chirality : 0.036 0.150 564 Planarity : 0.004 0.043 552 Dihedral : 4.950 40.532 658 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.71 % Allowed : 20.23 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.16 (0.41), residues: 413 helix: 2.77 (0.27), residues: 346 sheet: None (None), residues: 0 loop : -1.83 (0.62), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 500 HIS 0.001 0.001 HIS A 145 PHE 0.012 0.001 PHE A 496 TYR 0.019 0.001 TYR A 117 ARG 0.009 0.001 ARG A 301 Details of bonding type rmsd hydrogen bonds : bond 0.04859 ( 275) hydrogen bonds : angle 4.07404 ( 825) covalent geometry : bond 0.00380 ( 3424) covalent geometry : angle 0.52643 ( 4688) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ARG cc_start: 0.8078 (ttm170) cc_final: 0.7808 (ttm110) REVERT: A 321 TYR cc_start: 0.7668 (m-80) cc_final: 0.7406 (m-80) REVERT: A 388 CYS cc_start: 0.8704 (m) cc_final: 0.8281 (m) outliers start: 6 outliers final: 6 residues processed: 57 average time/residue: 0.3544 time to fit residues: 24.7963 Evaluate side-chains 61 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 406 TYR Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 510 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 27 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 11 optimal weight: 0.4980 chunk 39 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3608 r_free = 0.3608 target = 0.115525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.098271 restraints weight = 18171.927| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.42 r_work: 0.3251 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3424 Z= 0.152 Angle : 0.514 4.796 4688 Z= 0.275 Chirality : 0.035 0.144 564 Planarity : 0.004 0.048 552 Dihedral : 4.896 40.423 658 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.71 % Allowed : 20.23 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.21 (0.41), residues: 413 helix: 2.80 (0.27), residues: 346 sheet: None (None), residues: 0 loop : -1.83 (0.63), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 500 HIS 0.001 0.001 HIS A 145 PHE 0.011 0.001 PHE A 496 TYR 0.019 0.001 TYR A 117 ARG 0.007 0.001 ARG A 301 Details of bonding type rmsd hydrogen bonds : bond 0.04761 ( 275) hydrogen bonds : angle 4.05110 ( 825) covalent geometry : bond 0.00339 ( 3424) covalent geometry : angle 0.51414 ( 4688) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ARG cc_start: 0.8055 (ttm170) cc_final: 0.7785 (ttm110) REVERT: A 321 TYR cc_start: 0.7696 (m-80) cc_final: 0.7470 (m-80) REVERT: A 388 CYS cc_start: 0.8701 (m) cc_final: 0.8283 (m) REVERT: A 398 TYR cc_start: 0.8032 (m-80) cc_final: 0.7696 (m-10) outliers start: 6 outliers final: 6 residues processed: 59 average time/residue: 0.3413 time to fit residues: 24.5747 Evaluate side-chains 62 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 406 TYR Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 510 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 35 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3599 r_free = 0.3599 target = 0.114874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.097955 restraints weight = 18161.153| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.39 r_work: 0.3240 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3424 Z= 0.166 Angle : 0.526 4.886 4688 Z= 0.282 Chirality : 0.036 0.152 564 Planarity : 0.004 0.046 552 Dihedral : 4.997 40.622 658 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.99 % Allowed : 19.94 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.12 (0.41), residues: 413 helix: 2.71 (0.27), residues: 347 sheet: None (None), residues: 0 loop : -1.77 (0.63), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 500 HIS 0.001 0.001 HIS A 145 PHE 0.012 0.001 PHE A 496 TYR 0.019 0.001 TYR A 117 ARG 0.007 0.001 ARG A 301 Details of bonding type rmsd hydrogen bonds : bond 0.04899 ( 275) hydrogen bonds : angle 4.09480 ( 825) covalent geometry : bond 0.00372 ( 3424) covalent geometry : angle 0.52564 ( 4688) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3691.97 seconds wall clock time: 64 minutes 24.19 seconds (3864.19 seconds total)