Starting phenix.real_space_refine on Fri Aug 22 13:31:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ayb_43984/08_2025/9ayb_43984_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ayb_43984/08_2025/9ayb_43984.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ayb_43984/08_2025/9ayb_43984_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ayb_43984/08_2025/9ayb_43984_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ayb_43984/08_2025/9ayb_43984.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ayb_43984/08_2025/9ayb_43984.map" } resolution = 3.19 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= 0.001 sd= 0.025 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 16 5.16 5 C 2236 2.51 5 N 523 2.21 5 O 572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 3347 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3347 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 18, 'TRANS': 409} Chain breaks: 1 Time building chain proxies: 0.77, per 1000 atoms: 0.23 Number of scatterers: 3347 At special positions: 0 Unit cell: (61.254, 81.18, 66.42, 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 16 16.00 O 572 8.00 N 523 7.00 C 2236 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: 0.29 Conformation dependent library (CDL) restraints added in 89.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 0 sheets defined 89.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 37 through 68 removed outlier: 3.993A pdb=" N LEU A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA A 61 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL A 65 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 120 removed outlier: 4.833A pdb=" N PHE A 115 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N PHE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 134 Processing helix chain 'A' and resid 134 through 152 removed outlier: 4.596A pdb=" N LEU A 138 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE A 152 " --> pdb=" O VAL A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 160 Processing helix chain 'A' and resid 160 through 176 Processing helix chain 'A' and resid 177 through 187 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: 4.321A pdb=" N GLY A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ALA A 206 " --> pdb=" O SER A 202 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLN A 207 " --> pdb=" O TYR A 203 " (cutoff:3.500A) Proline residue: A 215 - end of helix removed outlier: 3.863A pdb=" N GLY A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 248 removed outlier: 4.077A pdb=" N PHE A 230 " --> pdb=" O TRP A 226 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 243 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL A 248 " --> pdb=" O TRP A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 Processing helix chain 'A' and resid 259 through 270 Processing helix chain 'A' and resid 281 through 288 Processing helix chain 'A' and resid 288 through 319 removed outlier: 3.670A pdb=" N TRP A 292 " --> pdb=" O SER A 288 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU A 312 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Proline residue: A 313 - end of helix Processing helix chain 'A' and resid 323 through 328 removed outlier: 3.684A pdb=" N ASN A 327 " --> pdb=" O ASN A 323 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 323 through 328' Processing helix chain 'A' and resid 328 through 355 Proline residue: A 334 - end of helix Processing helix chain 'A' and resid 359 through 382 Proline residue: A 375 - end of helix removed outlier: 3.594A pdb=" N PHE A 378 " --> pdb=" O GLY A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 403 removed outlier: 3.553A pdb=" N ALA A 392 " --> pdb=" O ASP A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 Processing helix chain 'A' and resid 409 through 411 No H-bonds generated for 'chain 'A' and resid 409 through 411' Processing helix chain 'A' and resid 412 through 418 removed outlier: 3.616A pdb=" N ASP A 416 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 434 Processing helix chain 'A' and resid 435 through 448 Proline residue: A 441 - end of helix Processing helix chain 'A' and resid 452 through 478 Processing helix chain 'A' and resid 483 through 487 245 hydrogen bonds defined for protein. 717 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: 0.39 Time building geometry restraints manager: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 986 1.34 - 1.46: 793 1.46 - 1.57: 1645 1.57 - 1.69: 0 1.69 - 1.81: 25 Bond restraints: 3449 Sorted by residual: bond pdb=" N VAL A 34 " pdb=" CA VAL A 34 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.70e+00 bond pdb=" C PRO A 191 " pdb=" O PRO A 191 " ideal model delta sigma weight residual 1.246 1.239 0.006 8.50e-03 1.38e+04 5.28e-01 bond pdb=" C TRP A 339 " pdb=" O TRP A 339 " ideal model delta sigma weight residual 1.236 1.245 -0.008 1.15e-02 7.56e+03 5.13e-01 bond pdb=" CA ILE A 435 " pdb=" C ILE A 435 " ideal model delta sigma weight residual 1.520 1.526 -0.006 8.80e-03 1.29e+04 4.73e-01 bond pdb=" N THR A 448 " pdb=" CA THR A 448 " ideal model delta sigma weight residual 1.464 1.457 0.007 1.05e-02 9.07e+03 4.40e-01 ... (remaining 3444 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.84: 4338 0.84 - 1.69: 305 1.69 - 2.53: 43 2.53 - 3.37: 9 3.37 - 4.21: 12 Bond angle restraints: 4707 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 120.24 122.57 -2.33 6.30e-01 2.52e+00 1.37e+01 angle pdb=" C ILE A 435 " pdb=" CA ILE A 435 " pdb=" CB ILE A 435 " ideal model delta sigma weight residual 114.35 111.13 3.22 1.06e+00 8.90e-01 9.25e+00 angle pdb=" N VAL A 283 " pdb=" CA VAL A 283 " pdb=" C VAL A 283 " ideal model delta sigma weight residual 112.35 109.91 2.44 1.20e+00 6.94e-01 4.15e+00 angle pdb=" C VAL A 283 " pdb=" CA VAL A 283 " pdb=" CB VAL A 283 " ideal model delta sigma weight residual 114.00 111.59 2.41 1.31e+00 5.83e-01 3.39e+00 angle pdb=" N SER A 408 " pdb=" CA SER A 408 " pdb=" C SER A 408 " ideal model delta sigma weight residual 113.72 111.56 2.16 1.30e+00 5.92e-01 2.75e+00 ... (remaining 4702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.88: 1730 14.88 - 29.76: 159 29.76 - 44.64: 49 44.64 - 59.52: 5 59.52 - 74.39: 1 Dihedral angle restraints: 1944 sinusoidal: 718 harmonic: 1226 Sorted by residual: 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 -164.00 -16.00 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" N LYS A 278 " pdb=" CA LYS A 278 " pdb=" CB LYS A 278 " pdb=" CG LYS A 278 " ideal model delta sinusoidal sigma weight residual -180.00 -121.39 -58.61 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA PHE A 305 " pdb=" C PHE A 305 " pdb=" N TYR A 306 " pdb=" CA TYR A 306 " ideal model delta harmonic sigma weight residual 180.00 164.72 15.28 0 5.00e+00 4.00e-02 9.34e+00 ... (remaining 1941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 316 0.027 - 0.054: 128 0.054 - 0.082: 66 0.082 - 0.109: 22 0.109 - 0.136: 3 Chirality restraints: 535 Sorted by residual: chirality pdb=" CA VAL A 280 " pdb=" N VAL A 280 " pdb=" C VAL A 280 " pdb=" CB VAL A 280 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA VAL A 34 " pdb=" N VAL A 34 " pdb=" C VAL A 34 " pdb=" CB VAL A 34 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA PHE A 305 " pdb=" N PHE A 305 " pdb=" C PHE A 305 " pdb=" CB PHE A 305 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.28e-01 ... (remaining 532 not shown) Planarity restraints: 571 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 162 " 0.024 5.00e-02 4.00e+02 3.71e-02 2.20e+00 pdb=" N PRO A 163 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 163 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 163 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 307 " -0.007 2.00e-02 2.50e+03 1.44e-02 2.08e+00 pdb=" C THR A 307 " 0.025 2.00e-02 2.50e+03 pdb=" O THR A 307 " -0.009 2.00e-02 2.50e+03 pdb=" N LEU A 308 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 374 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.66e+00 pdb=" N PRO A 375 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 375 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 375 " -0.018 5.00e-02 4.00e+02 ... (remaining 568 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1064 2.83 - 3.35: 3452 3.35 - 3.87: 5641 3.87 - 4.38: 6447 4.38 - 4.90: 11290 Nonbonded interactions: 27894 Sorted by model distance: nonbonded pdb=" O MET A 372 " pdb=" ND2 ASN A 467 " model vdw 2.313 3.120 nonbonded pdb=" O ASN A 357 " pdb=" OD1 ASN A 357 " model vdw 2.317 3.040 nonbonded pdb=" O CYS A 406 " pdb=" OG SER A 411 " model vdw 2.358 3.040 nonbonded pdb=" O THR A 448 " pdb=" OG1 THR A 448 " model vdw 2.388 3.040 nonbonded pdb=" NZ LYS A 136 " pdb=" O VAL A 248 " model vdw 2.439 3.120 ... (remaining 27889 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: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 3.980 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 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 : 0.003 0.031 3449 Z= 0.135 Angle : 0.518 4.214 4707 Z= 0.314 Chirality : 0.038 0.136 535 Planarity : 0.005 0.037 571 Dihedral : 12.732 74.394 1164 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.57 % Allowed : 7.93 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.23 (0.41), residues: 424 helix: 1.15 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -0.04 (0.61), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 353 TYR 0.009 0.001 TYR A 306 PHE 0.014 0.001 PHE A 232 TRP 0.008 0.001 TRP A 292 HIS 0.003 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 3449) covalent geometry : angle 0.51815 ( 4707) hydrogen bonds : bond 0.11550 ( 245) hydrogen bonds : angle 5.25640 ( 717) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.112 Fit side-chains REVERT: A 137 MET cc_start: 0.7869 (mmt) cc_final: 0.7605 (mmt) REVERT: A 175 GLU cc_start: 0.7972 (tt0) cc_final: 0.7638 (tt0) REVERT: A 182 MET cc_start: 0.7843 (tpp) cc_final: 0.7459 (tpt) REVERT: A 273 GLN cc_start: 0.8055 (mt0) cc_final: 0.7837 (mt0) outliers start: 2 outliers final: 2 residues processed: 37 average time/residue: 0.0581 time to fit residues: 2.6562 Evaluate side-chains 35 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 183 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3592 r_free = 0.3592 target = 0.139305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.097503 restraints weight = 3631.272| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.39 r_work: 0.2993 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.0778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3449 Z= 0.171 Angle : 0.552 4.871 4707 Z= 0.292 Chirality : 0.043 0.178 535 Planarity : 0.005 0.041 571 Dihedral : 5.402 50.104 459 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.12 % Allowed : 7.93 % Favored : 88.95 % 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: 1.49 (0.41), residues: 424 helix: 1.39 (0.29), residues: 330 sheet: None (None), residues: 0 loop : -0.26 (0.64), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 353 TYR 0.010 0.001 TYR A 119 PHE 0.018 0.002 PHE A 51 TRP 0.009 0.001 TRP A 292 HIS 0.001 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 3449) covalent geometry : angle 0.55204 ( 4707) hydrogen bonds : bond 0.05067 ( 245) hydrogen bonds : angle 4.44904 ( 717) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 29 time to evaluate : 0.123 Fit side-chains REVERT: A 175 GLU cc_start: 0.7947 (tt0) cc_final: 0.7684 (tt0) outliers start: 11 outliers final: 6 residues processed: 37 average time/residue: 0.0755 time to fit residues: 3.4459 Evaluate side-chains 33 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 316 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 7 optimal weight: 0.1980 chunk 21 optimal weight: 0.3980 chunk 10 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3535 r_free = 0.3535 target = 0.137584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.096381 restraints weight = 3614.106| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.26 r_work: 0.3020 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3449 Z= 0.124 Angle : 0.490 4.910 4707 Z= 0.259 Chirality : 0.040 0.124 535 Planarity : 0.005 0.043 571 Dihedral : 5.368 52.429 459 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.55 % Allowed : 8.50 % Favored : 88.95 % 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: 1.56 (0.41), residues: 424 helix: 1.52 (0.29), residues: 337 sheet: None (None), residues: 0 loop : -0.77 (0.61), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 168 TYR 0.009 0.001 TYR A 306 PHE 0.017 0.001 PHE A 51 TRP 0.009 0.001 TRP A 189 HIS 0.001 0.000 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 3449) covalent geometry : angle 0.49023 ( 4707) hydrogen bonds : bond 0.04333 ( 245) hydrogen bonds : angle 4.17673 ( 717) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.124 Fit side-chains REVERT: A 175 GLU cc_start: 0.7778 (tt0) cc_final: 0.7515 (tt0) outliers start: 9 outliers final: 5 residues processed: 36 average time/residue: 0.0525 time to fit residues: 2.3780 Evaluate side-chains 31 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 256 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 2 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3510 r_free = 0.3510 target = 0.135344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.094279 restraints weight = 3671.290| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.28 r_work: 0.2999 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3449 Z= 0.148 Angle : 0.507 5.018 4707 Z= 0.265 Chirality : 0.041 0.127 535 Planarity : 0.005 0.043 571 Dihedral : 5.325 53.496 459 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.55 % Allowed : 9.63 % Favored : 87.82 % 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 (0.40), residues: 424 helix: 1.48 (0.29), residues: 337 sheet: None (None), residues: 0 loop : -0.85 (0.57), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 168 TYR 0.009 0.001 TYR A 119 PHE 0.019 0.002 PHE A 51 TRP 0.009 0.001 TRP A 339 HIS 0.001 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 3449) covalent geometry : angle 0.50722 ( 4707) hydrogen bonds : bond 0.04456 ( 245) hydrogen bonds : angle 4.14766 ( 717) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 0.077 Fit side-chains REVERT: A 175 GLU cc_start: 0.7868 (tt0) cc_final: 0.7650 (tt0) outliers start: 9 outliers final: 7 residues processed: 31 average time/residue: 0.0538 time to fit residues: 2.1465 Evaluate side-chains 31 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 256 LYS Chi-restraints excluded: chain A residue 316 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 17 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3522 r_free = 0.3522 target = 0.135506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.094556 restraints weight = 3599.361| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.28 r_work: 0.2972 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3449 Z= 0.168 Angle : 0.525 5.624 4707 Z= 0.273 Chirality : 0.041 0.128 535 Planarity : 0.005 0.042 571 Dihedral : 5.298 51.109 459 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.83 % Allowed : 9.92 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.41 (0.40), residues: 424 helix: 1.45 (0.29), residues: 337 sheet: None (None), residues: 0 loop : -1.00 (0.56), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 168 TYR 0.009 0.001 TYR A 119 PHE 0.020 0.002 PHE A 51 TRP 0.010 0.001 TRP A 339 HIS 0.002 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 3449) covalent geometry : angle 0.52515 ( 4707) hydrogen bonds : bond 0.04676 ( 245) hydrogen bonds : angle 4.18954 ( 717) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 26 time to evaluate : 0.119 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 33 average time/residue: 0.0615 time to fit residues: 2.6017 Evaluate side-chains 32 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 256 LYS Chi-restraints excluded: chain A residue 316 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 17 optimal weight: 2.9990 chunk 38 optimal weight: 0.0670 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 21 optimal weight: 0.0050 chunk 26 optimal weight: 4.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.4732 ------------------------------------------------------------------------------- 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 = 0.3569 r_free = 0.3569 target = 0.139787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.098589 restraints weight = 3563.442| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.35 r_work: 0.3027 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3449 Z= 0.115 Angle : 0.476 5.037 4707 Z= 0.247 Chirality : 0.039 0.115 535 Planarity : 0.005 0.041 571 Dihedral : 5.364 57.043 459 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.98 % Allowed : 11.61 % Favored : 86.40 % 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: 1.68 (0.41), residues: 424 helix: 1.66 (0.29), residues: 336 sheet: None (None), residues: 0 loop : -0.96 (0.58), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 168 TYR 0.009 0.001 TYR A 306 PHE 0.017 0.001 PHE A 51 TRP 0.007 0.001 TRP A 339 HIS 0.000 0.000 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 3449) covalent geometry : angle 0.47642 ( 4707) hydrogen bonds : bond 0.04062 ( 245) hydrogen bonds : angle 4.05256 ( 717) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.116 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 33 average time/residue: 0.0717 time to fit residues: 2.9745 Evaluate side-chains 33 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 256 LYS Chi-restraints excluded: chain A residue 481 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 0.0570 chunk 27 optimal weight: 0.9980 chunk 16 optimal weight: 0.3980 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 = 0.3562 r_free = 0.3562 target = 0.139047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.097476 restraints weight = 3691.898| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.40 r_work: 0.2996 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3449 Z= 0.123 Angle : 0.485 5.054 4707 Z= 0.250 Chirality : 0.039 0.119 535 Planarity : 0.005 0.041 571 Dihedral : 5.186 53.256 459 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.55 % Allowed : 11.61 % Favored : 85.84 % 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: 1.69 (0.41), residues: 424 helix: 1.68 (0.29), residues: 337 sheet: None (None), residues: 0 loop : -1.02 (0.58), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 168 TYR 0.009 0.001 TYR A 306 PHE 0.018 0.001 PHE A 51 TRP 0.008 0.001 TRP A 339 HIS 0.001 0.000 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 3449) covalent geometry : angle 0.48542 ( 4707) hydrogen bonds : bond 0.04073 ( 245) hydrogen bonds : angle 4.01229 ( 717) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.080 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 33 average time/residue: 0.0579 time to fit residues: 2.3894 Evaluate side-chains 33 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 256 LYS Chi-restraints excluded: chain A residue 476 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 1 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 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 = 0.3515 r_free = 0.3515 target = 0.136318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.095385 restraints weight = 3708.405| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.31 r_work: 0.3013 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3449 Z= 0.140 Angle : 0.493 5.053 4707 Z= 0.255 Chirality : 0.040 0.118 535 Planarity : 0.005 0.041 571 Dihedral : 4.665 53.392 458 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.27 % Allowed : 11.33 % Favored : 86.40 % 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: 1.66 (0.41), residues: 424 helix: 1.64 (0.29), residues: 337 sheet: None (None), residues: 0 loop : -0.98 (0.58), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 168 TYR 0.008 0.001 TYR A 306 PHE 0.019 0.001 PHE A 51 TRP 0.009 0.001 TRP A 339 HIS 0.001 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 3449) covalent geometry : angle 0.49267 ( 4707) hydrogen bonds : bond 0.04250 ( 245) hydrogen bonds : angle 4.07723 ( 717) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.097 Fit side-chains REVERT: A 175 GLU cc_start: 0.7431 (tt0) cc_final: 0.7205 (tt0) outliers start: 8 outliers final: 7 residues processed: 32 average time/residue: 0.0619 time to fit residues: 2.5172 Evaluate side-chains 34 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 256 LYS Chi-restraints excluded: chain A residue 481 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.8980 chunk 32 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 21 optimal weight: 0.0980 chunk 30 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 = 0.3562 r_free = 0.3562 target = 0.139188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.098222 restraints weight = 3601.433| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.36 r_work: 0.3018 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3449 Z= 0.129 Angle : 0.483 5.047 4707 Z= 0.249 Chirality : 0.039 0.117 535 Planarity : 0.005 0.041 571 Dihedral : 4.650 53.593 458 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.98 % Allowed : 11.61 % Favored : 86.40 % 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: 1.72 (0.41), residues: 424 helix: 1.68 (0.29), residues: 337 sheet: None (None), residues: 0 loop : -0.91 (0.59), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 168 TYR 0.008 0.001 TYR A 306 PHE 0.017 0.001 PHE A 51 TRP 0.008 0.001 TRP A 339 HIS 0.002 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 3449) covalent geometry : angle 0.48311 ( 4707) hydrogen bonds : bond 0.04145 ( 245) hydrogen bonds : angle 4.04895 ( 717) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 26 time to evaluate : 0.122 Fit side-chains REVERT: A 175 GLU cc_start: 0.7552 (tt0) cc_final: 0.7337 (tt0) outliers start: 7 outliers final: 7 residues processed: 31 average time/residue: 0.0570 time to fit residues: 2.2640 Evaluate side-chains 33 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 26 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 256 LYS Chi-restraints excluded: chain A residue 481 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 13 optimal weight: 0.0060 chunk 27 optimal weight: 0.1980 chunk 18 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.4396 ------------------------------------------------------------------------------- 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 = 0.3588 r_free = 0.3588 target = 0.141719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.100674 restraints weight = 3562.474| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.36 r_work: 0.3050 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3449 Z= 0.110 Angle : 0.463 5.031 4707 Z= 0.239 Chirality : 0.038 0.117 535 Planarity : 0.005 0.041 571 Dihedral : 4.602 54.557 458 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.42 % Allowed : 12.18 % Favored : 86.40 % 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: 1.86 (0.41), residues: 424 helix: 1.77 (0.29), residues: 337 sheet: None (None), residues: 0 loop : -0.86 (0.60), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 168 TYR 0.009 0.001 TYR A 306 PHE 0.016 0.001 PHE A 51 TRP 0.009 0.001 TRP A 186 HIS 0.001 0.000 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 3449) covalent geometry : angle 0.46282 ( 4707) hydrogen bonds : bond 0.03854 ( 245) hydrogen bonds : angle 3.98798 ( 717) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.071 Fit side-chains REVERT: A 175 GLU cc_start: 0.7470 (tt0) cc_final: 0.7257 (tt0) outliers start: 5 outliers final: 4 residues processed: 29 average time/residue: 0.0587 time to fit residues: 2.1764 Evaluate side-chains 29 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 256 LYS Chi-restraints excluded: chain A residue 481 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 15 optimal weight: 0.0870 chunk 37 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 26 optimal weight: 0.0770 overall best weight: 0.6116 ------------------------------------------------------------------------------- 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 = 0.3540 r_free = 0.3540 target = 0.138516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.097062 restraints weight = 3716.512| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.42 r_work: 0.3026 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3449 Z= 0.121 Angle : 0.477 6.488 4707 Z= 0.245 Chirality : 0.039 0.118 535 Planarity : 0.005 0.041 571 Dihedral : 4.583 54.493 458 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.42 % Allowed : 12.46 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.41), residues: 424 helix: 1.76 (0.29), residues: 337 sheet: None (None), residues: 0 loop : -0.87 (0.60), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 168 TYR 0.009 0.001 TYR A 306 PHE 0.017 0.001 PHE A 51 TRP 0.008 0.001 TRP A 339 HIS 0.001 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 3449) covalent geometry : angle 0.47684 ( 4707) hydrogen bonds : bond 0.03984 ( 245) hydrogen bonds : angle 4.00966 ( 717) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 801.61 seconds wall clock time: 14 minutes 24.26 seconds (864.26 seconds total)