Starting phenix.real_space_refine on Fri Aug 22 13:32:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u3d_41858/08_2025/8u3d_41858.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u3d_41858/08_2025/8u3d_41858.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8u3d_41858/08_2025/8u3d_41858.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u3d_41858/08_2025/8u3d_41858.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u3d_41858/08_2025/8u3d_41858.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u3d_41858/08_2025/8u3d_41858.map" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.089 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: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2230 2.51 5 N 522 2.21 5 O 571 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 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: 3338 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3338 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 18, 'TRANS': 408} Chain breaks: 1 Time building chain proxies: 0.82, per 1000 atoms: 0.25 Number of scatterers: 3338 At special positions: 0 Unit cell: (57.27, 71.38, 81.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 571 8.00 N 522 7.00 C 2230 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.18 Conformation dependent library (CDL) restraints added in 81.6 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 776 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 0 sheets defined 87.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 37 through 68 removed outlier: 4.982A pdb=" N LEU A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N SER A 61 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL A 65 " --> pdb=" O SER A 61 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 120 removed outlier: 4.874A pdb=" N PHE A 115 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N PHE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 134 removed outlier: 3.893A pdb=" N GLY A 127 " --> pdb=" O GLN A 123 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 151 removed outlier: 3.911A pdb=" N LEU A 138 " --> pdb=" O GLY A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 160 removed outlier: 3.884A pdb=" N ASP A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY A 160 " --> pdb=" O ALA A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 177 removed outlier: 3.502A pdb=" N LEU A 164 " --> pdb=" O GLY A 160 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 190 removed outlier: 3.678A pdb=" N ALA A 181 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 193 No H-bonds generated for 'chain 'A' and resid 191 through 193' Processing helix chain 'A' and resid 194 through 224 removed outlier: 4.223A pdb=" N GLY A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ALA A 206 " --> pdb=" O SER A 202 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLN A 207 " --> pdb=" O TYR A 203 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) Proline residue: A 215 - end of helix Processing helix chain 'A' and resid 226 through 248 removed outlier: 4.134A pdb=" N PHE A 230 " --> pdb=" O TRP A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 271 Processing helix chain 'A' and resid 288 through 319 removed outlier: 4.115A pdb=" N ILE A 294 " --> pdb=" O PRO A 290 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR A 304 " --> pdb=" O SER A 300 " (cutoff:3.500A) Proline residue: A 313 - end of helix Processing helix chain 'A' and resid 323 through 356 removed outlier: 3.836A pdb=" N LEU A 333 " --> pdb=" O PHE A 329 " (cutoff:3.500A) Proline residue: A 334 - end of helix removed outlier: 3.661A pdb=" N GLY A 346 " --> pdb=" O MET A 342 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN A 347 " --> pdb=" O ILE A 343 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP A 350 " --> pdb=" O GLY A 346 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TRP A 356 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 385 Proline residue: A 375 - end of helix Processing helix chain 'A' and resid 388 through 403 removed outlier: 3.889A pdb=" N THR A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 Processing helix chain 'A' and resid 409 through 412 removed outlier: 3.539A pdb=" N ILE A 412 " --> pdb=" O GLY A 409 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 409 through 412' Processing helix chain 'A' and resid 413 through 418 removed outlier: 3.581A pdb=" N ALA A 418 " --> pdb=" O HIS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 434 Processing helix chain 'A' and resid 434 through 448 Proline residue: A 441 - end of helix Processing helix chain 'A' and resid 452 through 478 removed outlier: 3.629A pdb=" N TRP A 456 " --> pdb=" O THR A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 487 239 hydrogen bonds defined for protein. 705 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: 0.49 Time building geometry restraints manager: 0.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 973 1.34 - 1.45: 684 1.45 - 1.57: 1759 1.57 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 3440 Sorted by residual: bond pdb=" N ILE A 44 " pdb=" CA ILE A 44 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.32e-02 5.74e+03 7.33e+00 bond pdb=" N LEU A 45 " pdb=" CA LEU A 45 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.37e+00 bond pdb=" CB THR A 400 " pdb=" CG2 THR A 400 " ideal model delta sigma weight residual 1.521 1.446 0.075 3.30e-02 9.18e+02 5.13e+00 bond pdb=" N ALA A 43 " pdb=" CA ALA A 43 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.33e-02 5.65e+03 3.55e+00 bond pdb=" CA ALA A 43 " pdb=" CB ALA A 43 " ideal model delta sigma weight residual 1.530 1.499 0.031 1.68e-02 3.54e+03 3.42e+00 ... (remaining 3435 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 4418 1.53 - 3.06: 236 3.06 - 4.59: 32 4.59 - 6.12: 7 6.12 - 7.65: 1 Bond angle restraints: 4694 Sorted by residual: angle pdb=" C THR A 434 " pdb=" N ILE A 435 " pdb=" CA ILE A 435 " ideal model delta sigma weight residual 120.24 122.92 -2.68 6.30e-01 2.52e+00 1.81e+01 angle pdb=" C ILE A 435 " pdb=" CA ILE A 435 " pdb=" CB ILE A 435 " ideal model delta sigma weight residual 114.35 110.35 4.00 1.06e+00 8.90e-01 1.42e+01 angle pdb=" N LEU A 45 " pdb=" CA LEU A 45 " pdb=" C LEU A 45 " ideal model delta sigma weight residual 112.90 108.56 4.34 1.31e+00 5.83e-01 1.10e+01 angle pdb=" N VAL A 177 " pdb=" CA VAL A 177 " pdb=" CB VAL A 177 " ideal model delta sigma weight residual 111.23 105.88 5.35 1.65e+00 3.67e-01 1.05e+01 angle pdb=" C PRO A 449 " pdb=" N ASP A 450 " pdb=" CA ASP A 450 " ideal model delta sigma weight residual 121.54 116.13 5.41 1.91e+00 2.74e-01 8.01e+00 ... (remaining 4689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 1772 17.10 - 34.19: 140 34.19 - 51.29: 20 51.29 - 68.38: 2 68.38 - 85.48: 3 Dihedral angle restraints: 1937 sinusoidal: 716 harmonic: 1221 Sorted by residual: dihedral pdb=" CA PHE A 358 " pdb=" C PHE A 358 " pdb=" N SER A 359 " pdb=" CA SER A 359 " ideal model delta harmonic sigma weight residual 180.00 158.49 21.51 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA ASP A 450 " pdb=" C ASP A 450 " pdb=" N ASN A 451 " pdb=" CA ASN A 451 " ideal model delta harmonic sigma weight residual 180.00 160.74 19.26 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA TRP A 246 " pdb=" C TRP A 246 " pdb=" N LEU A 247 " pdb=" CA LEU A 247 " ideal model delta harmonic sigma weight residual -180.00 -162.32 -17.68 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 1934 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 335 0.044 - 0.089: 154 0.089 - 0.133: 38 0.133 - 0.177: 5 0.177 - 0.221: 1 Chirality restraints: 533 Sorted by residual: chirality pdb=" CB VAL A 177 " pdb=" CA VAL A 177 " pdb=" CG1 VAL A 177 " pdb=" CG2 VAL A 177 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA LEU A 289 " pdb=" N LEU A 289 " pdb=" C LEU A 289 " pdb=" CB LEU A 289 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.47e-01 chirality pdb=" CA ILE A 44 " pdb=" N ILE A 44 " pdb=" C ILE A 44 " pdb=" CB ILE A 44 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.06e-01 ... (remaining 530 not shown) Planarity restraints: 569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 289 " -0.037 5.00e-02 4.00e+02 5.52e-02 4.88e+00 pdb=" N PRO A 290 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 290 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 290 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 374 " 0.031 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PRO A 375 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 375 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 375 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 162 " -0.029 5.00e-02 4.00e+02 4.39e-02 3.09e+00 pdb=" N PRO A 163 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 163 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 163 " -0.025 5.00e-02 4.00e+02 ... (remaining 566 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 988 2.81 - 3.33: 3269 3.33 - 3.85: 5720 3.85 - 4.38: 7053 4.38 - 4.90: 11807 Nonbonded interactions: 28837 Sorted by model distance: nonbonded pdb=" OG1 THR A 304 " pdb=" OD1 ASN A 467 " model vdw 2.284 3.040 nonbonded pdb=" O SER A 213 " pdb=" OG SER A 217 " model vdw 2.301 3.040 nonbonded pdb=" O THR A 452 " pdb=" N GLU A 455 " model vdw 2.315 3.120 nonbonded pdb=" OH TYR A 40 " pdb=" OE2 GLU A 194 " model vdw 2.329 3.040 nonbonded pdb=" NZ LYS A 317 " pdb=" OE2 GLU A 318 " model vdw 2.345 3.120 ... (remaining 28832 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: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.310 Find NCS groups from input model: 0.010 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:5.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 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 : 0.009 0.075 3440 Z= 0.365 Angle : 0.781 7.654 4694 Z= 0.461 Chirality : 0.052 0.221 533 Planarity : 0.006 0.055 569 Dihedral : 12.533 85.479 1161 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % 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: -2.36 (0.35), residues: 423 helix: -1.21 (0.25), residues: 326 sheet: None (None), residues: 0 loop : -2.21 (0.55), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 168 TYR 0.021 0.002 TYR A 335 PHE 0.016 0.002 PHE A 299 TRP 0.021 0.002 TRP A 244 HIS 0.011 0.003 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00902 ( 3440) covalent geometry : angle 0.78113 ( 4694) hydrogen bonds : bond 0.12343 ( 239) hydrogen bonds : angle 5.70207 ( 705) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.121 Fit side-chains REVERT: A 239 PHE cc_start: 0.7041 (t80) cc_final: 0.6678 (m-10) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.3866 time to fit residues: 14.5392 Evaluate side-chains 32 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 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 255 HIS A 351 ASN A 414 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.125127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.096606 restraints weight = 3821.544| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.87 r_work: 0.2993 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3440 Z= 0.143 Angle : 0.582 8.591 4694 Z= 0.307 Chirality : 0.043 0.124 533 Planarity : 0.006 0.045 569 Dihedral : 4.868 20.738 455 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.99 % Allowed : 9.09 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.39), residues: 423 helix: 0.25 (0.28), residues: 327 sheet: None (None), residues: 0 loop : -1.88 (0.55), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 168 TYR 0.015 0.001 TYR A 335 PHE 0.014 0.001 PHE A 232 TRP 0.018 0.001 TRP A 244 HIS 0.005 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 3440) covalent geometry : angle 0.58208 ( 4694) hydrogen bonds : bond 0.04087 ( 239) hydrogen bonds : angle 4.64369 ( 705) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.118 Fit side-chains REVERT: A 194 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8510 (mt-10) REVERT: A 239 PHE cc_start: 0.7279 (t80) cc_final: 0.6363 (m-10) outliers start: 7 outliers final: 2 residues processed: 39 average time/residue: 0.3228 time to fit residues: 13.2541 Evaluate side-chains 31 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 199 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 21 optimal weight: 0.2980 chunk 10 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 HIS A 467 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.125129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.096879 restraints weight = 3876.775| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.87 r_work: 0.3001 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3440 Z= 0.136 Angle : 0.561 8.298 4694 Z= 0.293 Chirality : 0.042 0.131 533 Planarity : 0.006 0.052 569 Dihedral : 4.577 17.062 455 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.70 % Allowed : 11.36 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.40), residues: 423 helix: 0.88 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -1.73 (0.54), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 353 TYR 0.008 0.001 TYR A 335 PHE 0.013 0.001 PHE A 232 TRP 0.016 0.001 TRP A 244 HIS 0.004 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 3440) covalent geometry : angle 0.56096 ( 4694) hydrogen bonds : bond 0.03855 ( 239) hydrogen bonds : angle 4.48341 ( 705) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.090 Fit side-chains REVERT: A 194 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8469 (mt-10) REVERT: A 207 GLN cc_start: 0.8463 (mp10) cc_final: 0.8167 (mm-40) REVERT: A 239 PHE cc_start: 0.7260 (t80) cc_final: 0.6353 (m-10) outliers start: 6 outliers final: 3 residues processed: 39 average time/residue: 0.3500 time to fit residues: 14.2596 Evaluate side-chains 37 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 332 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 31 optimal weight: 0.0870 chunk 13 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.126034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.097953 restraints weight = 3807.440| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.85 r_work: 0.3018 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3440 Z= 0.126 Angle : 0.545 8.074 4694 Z= 0.283 Chirality : 0.042 0.119 533 Planarity : 0.006 0.054 569 Dihedral : 4.429 15.513 455 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.56 % Allowed : 11.93 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.41), residues: 423 helix: 1.22 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -1.49 (0.55), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 353 TYR 0.008 0.001 TYR A 335 PHE 0.014 0.001 PHE A 384 TRP 0.015 0.001 TRP A 244 HIS 0.003 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 3440) covalent geometry : angle 0.54509 ( 4694) hydrogen bonds : bond 0.03620 ( 239) hydrogen bonds : angle 4.40638 ( 705) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.082 Fit side-chains REVERT: A 207 GLN cc_start: 0.8480 (mp10) cc_final: 0.8185 (mm-40) REVERT: A 239 PHE cc_start: 0.7260 (t80) cc_final: 0.6356 (m-10) outliers start: 9 outliers final: 4 residues processed: 40 average time/residue: 0.4264 time to fit residues: 17.7383 Evaluate side-chains 35 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 332 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 0 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 21 optimal weight: 0.3980 chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.124862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.096712 restraints weight = 3838.873| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.86 r_work: 0.3002 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3440 Z= 0.144 Angle : 0.562 7.903 4694 Z= 0.291 Chirality : 0.043 0.120 533 Planarity : 0.006 0.055 569 Dihedral : 4.453 15.268 455 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.56 % Allowed : 13.07 % Favored : 84.38 % 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: 1.09 (0.41), residues: 423 helix: 1.33 (0.29), residues: 330 sheet: None (None), residues: 0 loop : -1.40 (0.55), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 353 TYR 0.010 0.001 TYR A 40 PHE 0.016 0.002 PHE A 384 TRP 0.015 0.001 TRP A 244 HIS 0.003 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 3440) covalent geometry : angle 0.56212 ( 4694) hydrogen bonds : bond 0.03863 ( 239) hydrogen bonds : angle 4.41533 ( 705) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.127 Fit side-chains REVERT: A 194 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8534 (mt-10) REVERT: A 207 GLN cc_start: 0.8512 (mp10) cc_final: 0.8202 (mm-40) REVERT: A 239 PHE cc_start: 0.7213 (t80) cc_final: 0.6364 (m-10) outliers start: 9 outliers final: 6 residues processed: 36 average time/residue: 0.3913 time to fit residues: 14.7589 Evaluate side-chains 39 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 342 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 32 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.125227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.097008 restraints weight = 3847.934| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.86 r_work: 0.3006 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3440 Z= 0.139 Angle : 0.559 7.876 4694 Z= 0.288 Chirality : 0.042 0.119 533 Planarity : 0.006 0.054 569 Dihedral : 4.422 15.155 455 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.56 % Allowed : 13.07 % Favored : 84.38 % 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: 1.35 (0.40), residues: 423 helix: 1.53 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -1.22 (0.54), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 353 TYR 0.009 0.001 TYR A 40 PHE 0.017 0.001 PHE A 384 TRP 0.015 0.001 TRP A 244 HIS 0.003 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 3440) covalent geometry : angle 0.55945 ( 4694) hydrogen bonds : bond 0.03773 ( 239) hydrogen bonds : angle 4.38449 ( 705) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.074 Fit side-chains REVERT: A 194 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8544 (mt-10) REVERT: A 207 GLN cc_start: 0.8514 (mp10) cc_final: 0.8206 (mm-40) REVERT: A 239 PHE cc_start: 0.7208 (t80) cc_final: 0.6364 (m-10) REVERT: A 417 ILE cc_start: 0.7726 (tp) cc_final: 0.7352 (tp) outliers start: 9 outliers final: 6 residues processed: 38 average time/residue: 0.3294 time to fit residues: 13.0624 Evaluate side-chains 39 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 342 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 19 optimal weight: 0.4980 chunk 12 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 32 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 467 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.125552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.097796 restraints weight = 4020.515| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.83 r_work: 0.2991 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3440 Z= 0.128 Angle : 0.548 7.850 4694 Z= 0.282 Chirality : 0.041 0.118 533 Planarity : 0.006 0.055 569 Dihedral : 4.341 14.928 455 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.56 % Allowed : 13.92 % Favored : 83.52 % 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: 1.48 (0.41), residues: 423 helix: 1.64 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -1.25 (0.54), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 353 TYR 0.008 0.001 TYR A 40 PHE 0.019 0.001 PHE A 384 TRP 0.015 0.001 TRP A 244 HIS 0.002 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 3440) covalent geometry : angle 0.54837 ( 4694) hydrogen bonds : bond 0.03605 ( 239) hydrogen bonds : angle 4.34055 ( 705) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.072 Fit side-chains REVERT: A 194 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8516 (mt-10) REVERT: A 239 PHE cc_start: 0.7301 (t80) cc_final: 0.6450 (m-10) REVERT: A 417 ILE cc_start: 0.7805 (tp) cc_final: 0.7439 (tp) outliers start: 9 outliers final: 6 residues processed: 37 average time/residue: 0.3373 time to fit residues: 13.0146 Evaluate side-chains 38 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 342 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 14 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.124930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.097023 restraints weight = 4010.486| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.84 r_work: 0.2983 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3440 Z= 0.135 Angle : 0.551 7.809 4694 Z= 0.284 Chirality : 0.042 0.118 533 Planarity : 0.006 0.054 569 Dihedral : 4.344 15.011 455 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.84 % Allowed : 13.64 % Favored : 83.52 % 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: 1.52 (0.41), residues: 423 helix: 1.67 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -1.24 (0.54), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 353 TYR 0.009 0.001 TYR A 40 PHE 0.020 0.001 PHE A 384 TRP 0.015 0.001 TRP A 244 HIS 0.002 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 3440) covalent geometry : angle 0.55129 ( 4694) hydrogen bonds : bond 0.03699 ( 239) hydrogen bonds : angle 4.34840 ( 705) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.106 Fit side-chains REVERT: A 239 PHE cc_start: 0.7313 (t80) cc_final: 0.6454 (m-10) REVERT: A 417 ILE cc_start: 0.7765 (tp) cc_final: 0.7412 (tp) outliers start: 10 outliers final: 6 residues processed: 40 average time/residue: 0.3561 time to fit residues: 14.8909 Evaluate side-chains 38 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 342 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 27 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 0.0060 chunk 6 optimal weight: 0.4980 chunk 39 optimal weight: 0.9980 chunk 35 optimal weight: 0.0870 overall best weight: 0.3974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.127525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.099633 restraints weight = 3944.953| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.84 r_work: 0.2986 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3440 Z= 0.113 Angle : 0.532 7.888 4694 Z= 0.273 Chirality : 0.041 0.115 533 Planarity : 0.005 0.055 569 Dihedral : 4.229 14.609 455 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.70 % Allowed : 15.34 % Favored : 82.95 % 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: 1.64 (0.41), residues: 423 helix: 1.74 (0.29), residues: 327 sheet: None (None), residues: 0 loop : -1.18 (0.55), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 353 TYR 0.007 0.001 TYR A 40 PHE 0.022 0.001 PHE A 384 TRP 0.014 0.001 TRP A 244 HIS 0.002 0.000 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 3440) covalent geometry : angle 0.53214 ( 4694) hydrogen bonds : bond 0.03302 ( 239) hydrogen bonds : angle 4.27316 ( 705) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.114 Fit side-chains REVERT: A 239 PHE cc_start: 0.7292 (t80) cc_final: 0.6433 (m-10) REVERT: A 417 ILE cc_start: 0.7776 (tp) cc_final: 0.7437 (tp) outliers start: 6 outliers final: 2 residues processed: 38 average time/residue: 0.3258 time to fit residues: 13.0326 Evaluate side-chains 36 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 324 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 34 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.125495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.097604 restraints weight = 3981.145| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.85 r_work: 0.2990 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3440 Z= 0.137 Angle : 0.551 7.777 4694 Z= 0.284 Chirality : 0.042 0.122 533 Planarity : 0.006 0.055 569 Dihedral : 4.286 15.036 455 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.14 % Allowed : 16.48 % Favored : 82.39 % 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: 1.61 (0.41), residues: 423 helix: 1.75 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -1.27 (0.54), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 353 TYR 0.009 0.001 TYR A 40 PHE 0.023 0.002 PHE A 384 TRP 0.014 0.001 TRP A 244 HIS 0.002 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 3440) covalent geometry : angle 0.55095 ( 4694) hydrogen bonds : bond 0.03668 ( 239) hydrogen bonds : angle 4.31462 ( 705) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.082 Fit side-chains REVERT: A 239 PHE cc_start: 0.7312 (t80) cc_final: 0.6450 (m-10) REVERT: A 417 ILE cc_start: 0.7813 (tp) cc_final: 0.7462 (tp) outliers start: 4 outliers final: 2 residues processed: 36 average time/residue: 0.3508 time to fit residues: 13.1808 Evaluate side-chains 33 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 324 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 11 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 4 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN A 467 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.125207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.097338 restraints weight = 4050.851| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.86 r_work: 0.2985 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3440 Z= 0.139 Angle : 0.555 7.747 4694 Z= 0.287 Chirality : 0.043 0.118 533 Planarity : 0.006 0.055 569 Dihedral : 4.314 14.971 455 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.14 % Allowed : 16.48 % Favored : 82.39 % 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: 1.62 (0.41), residues: 423 helix: 1.76 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -1.29 (0.54), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 353 TYR 0.009 0.001 TYR A 40 PHE 0.024 0.002 PHE A 384 TRP 0.014 0.001 TRP A 244 HIS 0.002 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 3440) covalent geometry : angle 0.55465 ( 4694) hydrogen bonds : bond 0.03719 ( 239) hydrogen bonds : angle 4.34552 ( 705) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1033.58 seconds wall clock time: 18 minutes 19.32 seconds (1099.32 seconds total)