Starting phenix.real_space_refine on Tue Aug 4 14:25:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/26vc_80905/08_2026/26vc_80905.cif Found real_map, /net/cci-nas-00/data/ceres_data/26vc_80905/08_2026/26vc_80905.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/26vc_80905/08_2026/26vc_80905.map" default_real_map = "/net/cci-nas-00/data/ceres_data/26vc_80905/08_2026/26vc_80905.map" model { file = "/net/cci-nas-00/data/ceres_data/26vc_80905/08_2026/26vc_80905.cif" } default_model = "/net/cci-nas-00/data/ceres_data/26vc_80905/08_2026/26vc_80905.cif" } resolution = 4.1 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= 0.000 sd= 0.017 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 34 5.16 5 C 2567 2.51 5 N 609 2.21 5 O 646 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-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3856 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3844 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 22, 'TRANS': 477} Chain breaks: 1 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'LPA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.71, per 1000 atoms: 0.18 Number of scatterers: 3856 At special positions: 0 Unit cell: (79.92, 66.6, 78.44, 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 34 16.00 O 646 8.00 N 609 7.00 C 2567 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 85.8 milliseconds 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 902 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 0 sheets defined 82.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing helix chain 'A' and resid 29 through 48 removed outlier: 4.007A pdb=" N SER A 39 " --> pdb=" O LEU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 62 Processing helix chain 'A' and resid 63 through 65 No H-bonds generated for 'chain 'A' and resid 63 through 65' Processing helix chain 'A' and resid 68 through 79 removed outlier: 4.496A pdb=" N PHE A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 96 Proline residue: A 89 - end of helix Processing helix chain 'A' and resid 97 through 104 removed outlier: 3.767A pdb=" N PHE A 101 " --> pdb=" O GLN A 98 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A 102 " --> pdb=" O TYR A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 116 Proline residue: A 113 - end of helix Processing helix chain 'A' and resid 116 through 124 removed outlier: 3.984A pdb=" N VAL A 120 " --> pdb=" O ILE A 116 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 137 removed outlier: 3.892A pdb=" N GLU A 134 " --> pdb=" O TYR A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 173 removed outlier: 3.717A pdb=" N ARG A 142 " --> pdb=" O ASN A 138 " (cutoff:3.500A) Proline residue: A 164 - end of helix Processing helix chain 'A' and resid 175 through 195 removed outlier: 3.845A pdb=" N SER A 179 " --> pdb=" O ASP A 175 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TYR A 190 " --> pdb=" O VAL A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 226 Processing helix chain 'A' and resid 227 through 238 removed outlier: 3.899A pdb=" N HIS A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 271 Processing helix chain 'A' and resid 274 through 282 removed outlier: 4.407A pdb=" N ARG A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 322 removed outlier: 4.425A pdb=" N PHE A 298 " --> pdb=" O CYS A 294 " (cutoff:3.500A) Proline residue: A 299 - end of helix Processing helix chain 'A' and resid 334 through 345 removed outlier: 4.202A pdb=" N LEU A 338 " --> pdb=" O ASP A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 383 removed outlier: 3.947A pdb=" N ILE A 383 " --> pdb=" O MET A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 417 Processing helix chain 'A' and resid 422 through 434 Processing helix chain 'A' and resid 434 through 448 removed outlier: 3.912A pdb=" N LEU A 438 " --> pdb=" O VAL A 434 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 477 removed outlier: 3.549A pdb=" N THR A 477 " --> pdb=" O GLY A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 549 Processing helix chain 'A' and resid 564 through 569 removed outlier: 3.677A pdb=" N LYS A 568 " --> pdb=" O PRO A 564 " (cutoff:3.500A) 288 hydrogen bonds defined for protein. 855 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: 0.63 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 - 1.38: 1415 1.38 - 1.54: 2435 1.54 - 1.70: 56 1.70 - 1.86: 53 1.86 - 2.02: 1 Bond restraints: 3960 Sorted by residual: bond pdb=" C6 LPA A 701 " pdb=" S6 LPA A 701 " ideal model delta sigma weight residual 1.853 1.782 0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" S6 LPA A 701 " pdb=" S8 LPA A 701 " ideal model delta sigma weight residual 2.081 2.016 0.065 2.00e-02 2.50e+03 1.04e+01 bond pdb=" C PRO A 453 " pdb=" N PRO A 454 " ideal model delta sigma weight residual 1.336 1.359 -0.023 1.23e-02 6.61e+03 3.49e+00 bond pdb=" C8 LPA A 701 " pdb=" S8 LPA A 701 " ideal model delta sigma weight residual 1.816 1.784 0.032 2.00e-02 2.50e+03 2.61e+00 bond pdb=" CA ALA A 163 " pdb=" C ALA A 163 " ideal model delta sigma weight residual 1.520 1.540 -0.020 1.23e-02 6.61e+03 2.56e+00 ... (remaining 3955 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 5077 1.79 - 3.57: 265 3.57 - 5.36: 35 5.36 - 7.15: 8 7.15 - 8.94: 7 Bond angle restraints: 5392 Sorted by residual: angle pdb=" N PRO A 453 " pdb=" CA PRO A 453 " pdb=" C PRO A 453 " ideal model delta sigma weight residual 110.70 115.04 -4.34 1.22e+00 6.72e-01 1.27e+01 angle pdb=" CA PRO A 453 " pdb=" C PRO A 453 " pdb=" N PRO A 454 " ideal model delta sigma weight residual 117.93 122.14 -4.21 1.20e+00 6.94e-01 1.23e+01 angle pdb=" N PHE A 117 " pdb=" CA PHE A 117 " pdb=" C PHE A 117 " ideal model delta sigma weight residual 111.36 114.41 -3.05 1.09e+00 8.42e-01 7.84e+00 angle pdb=" CA ILE A 112 " pdb=" C ILE A 112 " pdb=" N PRO A 113 " ideal model delta sigma weight residual 118.88 123.08 -4.20 1.54e+00 4.22e-01 7.45e+00 angle pdb=" CA PRO A 454 " pdb=" N PRO A 454 " pdb=" CD PRO A 454 " ideal model delta sigma weight residual 112.00 108.39 3.61 1.40e+00 5.10e-01 6.63e+00 ... (remaining 5387 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.92: 2217 21.92 - 43.83: 42 43.83 - 65.74: 6 65.74 - 87.65: 4 87.65 - 109.56: 1 Dihedral angle restraints: 2270 sinusoidal: 846 harmonic: 1424 Sorted by residual: dihedral pdb=" CA CYS A 48 " pdb=" C CYS A 48 " pdb=" N ARG A 49 " pdb=" CA ARG A 49 " ideal model delta harmonic sigma weight residual 180.00 161.06 18.94 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" C3 LPA A 701 " pdb=" C4 LPA A 701 " pdb=" C5 LPA A 701 " pdb=" C6 LPA A 701 " ideal model delta sinusoidal sigma weight residual 176.44 -74.00 -109.56 1 3.00e+01 1.11e-03 1.42e+01 dihedral pdb=" CA GLY A 195 " pdb=" C GLY A 195 " pdb=" N LEU A 196 " pdb=" CA LEU A 196 " ideal model delta harmonic sigma weight residual 180.00 -161.68 -18.32 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 2267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 483 0.063 - 0.126: 132 0.126 - 0.189: 12 0.189 - 0.252: 0 0.252 - 0.315: 1 Chirality restraints: 628 Sorted by residual: chirality pdb=" CB ILE A 311 " pdb=" CA ILE A 311 " pdb=" CG1 ILE A 311 " pdb=" CG2 ILE A 311 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" CB VAL A 278 " pdb=" CA VAL A 278 " pdb=" CG1 VAL A 278 " pdb=" CG2 VAL A 278 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.69e-01 chirality pdb=" CG LEU A 338 " pdb=" CB LEU A 338 " pdb=" CD1 LEU A 338 " pdb=" CD2 LEU A 338 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.47e-01 ... (remaining 625 not shown) Planarity restraints: 658 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 384 " -0.037 5.00e-02 4.00e+02 5.46e-02 4.76e+00 pdb=" N PRO A 385 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 385 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 385 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 332 " 0.033 5.00e-02 4.00e+02 5.05e-02 4.08e+00 pdb=" N PRO A 333 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 333 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 333 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 247 " 0.033 5.00e-02 4.00e+02 5.04e-02 4.06e+00 pdb=" N PRO A 248 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 248 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 248 " 0.028 5.00e-02 4.00e+02 ... (remaining 655 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 1327 2.87 - 3.38: 3757 3.38 - 3.89: 6185 3.89 - 4.39: 6620 4.39 - 4.90: 11571 Nonbonded interactions: 29460 Sorted by model distance: nonbonded pdb=" O GLY A 362 " pdb=" OG SER A 365 " model vdw 2.365 3.040 nonbonded pdb=" O LEU A 168 " pdb=" OG1 THR A 172 " model vdw 2.368 3.040 nonbonded pdb=" O GLY A 184 " pdb=" OG1 THR A 188 " model vdw 2.387 3.040 nonbonded pdb=" O ALA A 357 " pdb=" OG SER A 361 " model vdw 2.395 3.040 nonbonded pdb=" O ILE A 383 " pdb=" N PHE A 387 " model vdw 2.406 3.120 ... (remaining 29455 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 group one per residue 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: 1.310 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.980 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 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 : 0.005 0.071 3960 Z= 0.252 Angle : 0.927 8.937 5392 Z= 0.499 Chirality : 0.054 0.315 628 Planarity : 0.008 0.055 658 Dihedral : 10.965 109.564 1368 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.97 (0.31), residues: 496 helix: -1.46 (0.22), residues: 367 sheet: None (None), residues: 0 loop : -3.06 (0.51), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 280 TYR 0.030 0.002 TYR A 106 PHE 0.023 0.002 PHE A 404 TRP 0.025 0.002 TRP A 177 HIS 0.003 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.25 ( 3960) covalent geometry : angle 0.92678 / 0.50 ( 5392) hydrogen bonds : bond 0.12584 / 8.28 ( 288) hydrogen bonds : angle 5.92834 / 4.29 ( 855) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.5505 (mt) cc_final: 0.5049 (mm) REVERT: A 95 PHE cc_start: 0.7723 (m-80) cc_final: 0.7488 (m-80) REVERT: A 157 MET cc_start: 0.8994 (tmm) cc_final: 0.8434 (tmm) REVERT: A 166 LEU cc_start: 0.8885 (tt) cc_final: 0.8617 (tp) REVERT: A 232 TRP cc_start: 0.6643 (t-100) cc_final: 0.6421 (t60) REVERT: A 275 GLN cc_start: 0.8003 (tp40) cc_final: 0.7619 (tp40) REVERT: A 315 MET cc_start: 0.8947 (ttp) cc_final: 0.8310 (ttp) REVERT: A 346 LYS cc_start: 0.8098 (pttp) cc_final: 0.7788 (ptmm) REVERT: A 397 MET cc_start: 0.6300 (mtm) cc_final: 0.5844 (mtt) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.0426 time to fit residues: 8.7631 Evaluate side-chains 108 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 0.0870 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.0070 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 238 HIS A 452 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.174122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.150988 restraints weight = 6806.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.155486 restraints weight = 3576.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.158567 restraints weight = 2254.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.160642 restraints weight = 1597.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.162260 restraints weight = 1240.715| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3960 Z= 0.134 Angle : 0.609 6.772 5392 Z= 0.321 Chirality : 0.039 0.119 628 Planarity : 0.005 0.045 658 Dihedral : 8.817 126.360 553 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.37), residues: 496 helix: 0.39 (0.26), residues: 365 sheet: None (None), residues: 0 loop : -2.66 (0.53), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 94 TYR 0.016 0.002 TYR A 99 PHE 0.037 0.002 PHE A 404 TRP 0.018 0.001 TRP A 177 HIS 0.001 0.000 HIS A 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 ( 3960) covalent geometry : angle 0.60940 / 0.32 ( 5392) hydrogen bonds : bond 0.04935 / 3.25 ( 288) hydrogen bonds : angle 4.55709 / 3.30 ( 855) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.082 Fit side-chains revert: symmetry clash REVERT: A 44 LEU cc_start: 0.5371 (mt) cc_final: 0.5034 (tp) REVERT: A 63 ASP cc_start: 0.8101 (t0) cc_final: 0.7841 (t0) REVERT: A 153 MET cc_start: 0.8614 (mmt) cc_final: 0.8282 (tpp) REVERT: A 157 MET cc_start: 0.9066 (tmm) cc_final: 0.8483 (tmm) REVERT: A 315 MET cc_start: 0.8849 (ttp) cc_final: 0.8370 (ttp) REVERT: A 346 LYS cc_start: 0.8079 (pttp) cc_final: 0.7723 (ptmm) REVERT: A 371 PHE cc_start: 0.8207 (m-10) cc_final: 0.7998 (m-10) REVERT: A 397 MET cc_start: 0.6319 (mtm) cc_final: 0.5928 (mtt) REVERT: A 552 MET cc_start: 0.7730 (tpp) cc_final: 0.7431 (tpp) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.0435 time to fit residues: 7.0582 Evaluate side-chains 112 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 48 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 22 optimal weight: 0.1980 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 534 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.172759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.150014 restraints weight = 6890.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.154338 restraints weight = 3669.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.157262 restraints weight = 2324.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.159118 restraints weight = 1673.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.160515 restraints weight = 1334.545| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3960 Z= 0.131 Angle : 0.588 6.713 5392 Z= 0.303 Chirality : 0.039 0.111 628 Planarity : 0.004 0.044 658 Dihedral : 8.113 115.560 553 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.39), residues: 496 helix: 1.13 (0.27), residues: 366 sheet: None (None), residues: 0 loop : -2.30 (0.55), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 142 TYR 0.014 0.001 TYR A 190 PHE 0.017 0.001 PHE A 151 TRP 0.016 0.001 TRP A 177 HIS 0.001 0.000 HIS A 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 ( 3960) covalent geometry : angle 0.58818 / 0.30 ( 5392) hydrogen bonds : bond 0.04644 / 3.10 ( 288) hydrogen bonds : angle 4.27844 / 3.11 ( 855) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.100 Fit side-chains revert: symmetry clash REVERT: A 44 LEU cc_start: 0.5453 (mt) cc_final: 0.4988 (tp) REVERT: A 115 HIS cc_start: 0.8303 (m-70) cc_final: 0.8022 (m-70) REVERT: A 131 GLU cc_start: 0.8513 (mt-10) cc_final: 0.7931 (mt-10) REVERT: A 142 ARG cc_start: 0.8459 (ttt90) cc_final: 0.7588 (ttt90) REVERT: A 157 MET cc_start: 0.9212 (tmm) cc_final: 0.8334 (tmm) REVERT: A 275 GLN cc_start: 0.7876 (tp40) cc_final: 0.7352 (tp40) REVERT: A 315 MET cc_start: 0.8873 (ttp) cc_final: 0.8397 (ttm) REVERT: A 337 VAL cc_start: 0.8788 (t) cc_final: 0.8586 (t) REVERT: A 346 LYS cc_start: 0.8162 (pttp) cc_final: 0.7759 (ptmm) REVERT: A 371 PHE cc_start: 0.8233 (m-10) cc_final: 0.8008 (m-10) REVERT: A 397 MET cc_start: 0.6301 (mtm) cc_final: 0.5989 (mtt) REVERT: A 452 ASN cc_start: 0.7977 (m-40) cc_final: 0.7433 (m110) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.0538 time to fit residues: 8.7345 Evaluate side-chains 106 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 9 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 36 optimal weight: 0.2980 chunk 39 optimal weight: 0.0370 chunk 14 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 GLN A 372 ASN A 534 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.174031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.150183 restraints weight = 7074.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.154590 restraints weight = 3802.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.157602 restraints weight = 2432.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.159417 restraints weight = 1765.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.161055 restraints weight = 1424.204| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3960 Z= 0.121 Angle : 0.574 6.741 5392 Z= 0.291 Chirality : 0.039 0.108 628 Planarity : 0.004 0.046 658 Dihedral : 7.566 109.100 553 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.39), residues: 496 helix: 1.52 (0.27), residues: 366 sheet: None (None), residues: 0 loop : -2.20 (0.54), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 142 TYR 0.013 0.001 TYR A 190 PHE 0.016 0.001 PHE A 151 TRP 0.013 0.001 TRP A 177 HIS 0.001 0.000 HIS A 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 ( 3960) covalent geometry : angle 0.57420 / 0.29 ( 5392) hydrogen bonds : bond 0.04392 / 2.89 ( 288) hydrogen bonds : angle 4.21983 / 3.07 ( 855) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.084 Fit side-chains revert: symmetry clash REVERT: A 63 ASP cc_start: 0.8127 (t0) cc_final: 0.7812 (m-30) REVERT: A 115 HIS cc_start: 0.8293 (m-70) cc_final: 0.7966 (m-70) REVERT: A 130 TYR cc_start: 0.8318 (m-80) cc_final: 0.7843 (m-10) REVERT: A 131 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8027 (mt-10) REVERT: A 142 ARG cc_start: 0.8398 (ttt90) cc_final: 0.7489 (ttt90) REVERT: A 157 MET cc_start: 0.9061 (tmm) cc_final: 0.8685 (tmm) REVERT: A 166 LEU cc_start: 0.9007 (tt) cc_final: 0.8782 (tp) REVERT: A 196 LEU cc_start: 0.9387 (tp) cc_final: 0.9161 (tp) REVERT: A 275 GLN cc_start: 0.7801 (tp40) cc_final: 0.7367 (tp40) REVERT: A 315 MET cc_start: 0.8820 (ttp) cc_final: 0.8616 (ttp) REVERT: A 345 LEU cc_start: 0.8936 (mp) cc_final: 0.8706 (mp) REVERT: A 346 LYS cc_start: 0.8221 (pttp) cc_final: 0.7887 (ptmm) REVERT: A 371 PHE cc_start: 0.8230 (m-10) cc_final: 0.8010 (m-10) REVERT: A 397 MET cc_start: 0.6413 (mtm) cc_final: 0.6130 (mtt) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.0435 time to fit residues: 7.9896 Evaluate side-chains 108 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 5 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 534 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.168751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.145537 restraints weight = 7202.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.149813 restraints weight = 3869.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.152721 restraints weight = 2480.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.154720 restraints weight = 1792.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.156047 restraints weight = 1422.030| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3960 Z= 0.161 Angle : 0.663 7.128 5392 Z= 0.323 Chirality : 0.041 0.119 628 Planarity : 0.004 0.044 658 Dihedral : 7.109 99.753 553 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.40), residues: 496 helix: 1.50 (0.28), residues: 368 sheet: None (None), residues: 0 loop : -2.04 (0.57), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 285 TYR 0.014 0.002 TYR A 295 PHE 0.018 0.002 PHE A 149 TRP 0.014 0.001 TRP A 177 HIS 0.002 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 ( 3960) covalent geometry : angle 0.66295 / 0.32 ( 5392) hydrogen bonds : bond 0.04891 / 3.22 ( 288) hydrogen bonds : angle 4.24515 / 3.08 ( 855) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.141 Fit side-chains REVERT: A 115 HIS cc_start: 0.8348 (m-70) cc_final: 0.7994 (m-70) REVERT: A 131 GLU cc_start: 0.8671 (mt-10) cc_final: 0.7934 (mt-10) REVERT: A 142 ARG cc_start: 0.8550 (ttt90) cc_final: 0.7635 (ttt90) REVERT: A 157 MET cc_start: 0.9000 (tmm) cc_final: 0.8632 (tmm) REVERT: A 166 LEU cc_start: 0.8950 (tt) cc_final: 0.8696 (tp) REVERT: A 196 LEU cc_start: 0.9420 (tp) cc_final: 0.9212 (tp) REVERT: A 275 GLN cc_start: 0.7965 (tp40) cc_final: 0.7487 (tp40) REVERT: A 346 LYS cc_start: 0.8397 (pttp) cc_final: 0.7972 (ptmm) REVERT: A 356 ILE cc_start: 0.8859 (mm) cc_final: 0.8632 (mm) REVERT: A 371 PHE cc_start: 0.8345 (m-10) cc_final: 0.8121 (m-10) REVERT: A 397 MET cc_start: 0.6377 (mtm) cc_final: 0.6077 (mtt) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.0554 time to fit residues: 8.4313 Evaluate side-chains 103 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 18 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 534 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.170749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.147183 restraints weight = 7256.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.151563 restraints weight = 3867.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.154502 restraints weight = 2463.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.156020 restraints weight = 1783.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.157911 restraints weight = 1461.872| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3960 Z= 0.138 Angle : 0.620 5.932 5392 Z= 0.310 Chirality : 0.040 0.116 628 Planarity : 0.004 0.058 658 Dihedral : 7.000 98.502 553 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.40), residues: 496 helix: 1.62 (0.28), residues: 368 sheet: None (None), residues: 0 loop : -2.01 (0.57), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 142 TYR 0.018 0.001 TYR A 132 PHE 0.017 0.001 PHE A 149 TRP 0.012 0.001 TRP A 177 HIS 0.002 0.001 HIS A 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 ( 3960) covalent geometry : angle 0.62021 / 0.31 ( 5392) hydrogen bonds : bond 0.04704 / 3.08 ( 288) hydrogen bonds : angle 4.27652 / 3.09 ( 855) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.139 Fit side-chains revert: symmetry clash REVERT: A 115 HIS cc_start: 0.8331 (m-70) cc_final: 0.7974 (m-70) REVERT: A 131 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8152 (mt-10) REVERT: A 142 ARG cc_start: 0.8469 (ttt90) cc_final: 0.7623 (ttt90) REVERT: A 157 MET cc_start: 0.8953 (tmm) cc_final: 0.8523 (tmm) REVERT: A 166 LEU cc_start: 0.8941 (tt) cc_final: 0.8679 (tp) REVERT: A 196 LEU cc_start: 0.9380 (tp) cc_final: 0.9179 (tp) REVERT: A 210 MET cc_start: 0.6727 (ttm) cc_final: 0.6467 (mtp) REVERT: A 271 TYR cc_start: 0.8343 (m-10) cc_final: 0.8136 (m-10) REVERT: A 275 GLN cc_start: 0.7885 (tp40) cc_final: 0.7328 (tp40) REVERT: A 315 MET cc_start: 0.8951 (ttp) cc_final: 0.8510 (ttm) REVERT: A 356 ILE cc_start: 0.8833 (mm) cc_final: 0.8626 (mm) REVERT: A 397 MET cc_start: 0.6433 (mtm) cc_final: 0.6187 (mtt) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.0619 time to fit residues: 9.5888 Evaluate side-chains 101 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 2 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 chunk 43 optimal weight: 0.9980 chunk 36 optimal weight: 0.0020 chunk 27 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 534 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.172653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.148260 restraints weight = 7222.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.152791 restraints weight = 3943.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.155736 restraints weight = 2541.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.157984 restraints weight = 1858.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.159516 restraints weight = 1462.444| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3960 Z= 0.130 Angle : 0.619 6.027 5392 Z= 0.305 Chirality : 0.040 0.113 628 Planarity : 0.004 0.051 658 Dihedral : 6.693 93.583 553 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.39), residues: 496 helix: 1.57 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -1.77 (0.59), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 142 TYR 0.016 0.001 TYR A 132 PHE 0.020 0.001 PHE A 149 TRP 0.011 0.001 TRP A 177 HIS 0.002 0.001 HIS A 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 3960) covalent geometry : angle 0.61870 / 0.30 ( 5392) hydrogen bonds : bond 0.04605 / 3.02 ( 288) hydrogen bonds : angle 4.29147 / 3.10 ( 855) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.134 Fit side-chains REVERT: A 63 ASP cc_start: 0.7913 (t0) cc_final: 0.7672 (t0) REVERT: A 115 HIS cc_start: 0.8305 (m-70) cc_final: 0.7936 (m-70) REVERT: A 131 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8133 (mt-10) REVERT: A 142 ARG cc_start: 0.8486 (ttt90) cc_final: 0.7627 (ttt90) REVERT: A 157 MET cc_start: 0.9016 (tmm) cc_final: 0.8503 (tmm) REVERT: A 166 LEU cc_start: 0.8939 (tt) cc_final: 0.8662 (tp) REVERT: A 196 LEU cc_start: 0.9416 (tp) cc_final: 0.9126 (tp) REVERT: A 268 LEU cc_start: 0.7774 (tp) cc_final: 0.7523 (tp) REVERT: A 275 GLN cc_start: 0.7811 (tp40) cc_final: 0.7276 (tp40) REVERT: A 315 MET cc_start: 0.8929 (ttp) cc_final: 0.8464 (ttm) REVERT: A 371 PHE cc_start: 0.8297 (m-10) cc_final: 0.8085 (m-10) REVERT: A 380 GLU cc_start: 0.8625 (tp30) cc_final: 0.8405 (tp30) REVERT: A 397 MET cc_start: 0.6472 (mtm) cc_final: 0.6045 (mtt) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.0472 time to fit residues: 7.4262 Evaluate side-chains 101 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 30 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 534 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.172307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.148371 restraints weight = 7071.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.152774 restraints weight = 3891.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.155914 restraints weight = 2536.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.158019 restraints weight = 1836.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.159563 restraints weight = 1446.972| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3960 Z= 0.139 Angle : 0.621 7.070 5392 Z= 0.309 Chirality : 0.040 0.133 628 Planarity : 0.004 0.049 658 Dihedral : 6.645 94.661 553 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.39), residues: 496 helix: 1.54 (0.27), residues: 376 sheet: None (None), residues: 0 loop : -2.25 (0.57), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 142 TYR 0.015 0.001 TYR A 132 PHE 0.032 0.001 PHE A 149 TRP 0.010 0.001 TRP A 177 HIS 0.002 0.001 HIS A 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 ( 3960) covalent geometry : angle 0.62139 / 0.31 ( 5392) hydrogen bonds : bond 0.04662 / 3.04 ( 288) hydrogen bonds : angle 4.30947 / 3.12 ( 855) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.132 Fit side-chains revert: symmetry clash REVERT: A 63 ASP cc_start: 0.7907 (t0) cc_final: 0.7680 (t0) REVERT: A 115 HIS cc_start: 0.8306 (m-70) cc_final: 0.7936 (m-70) REVERT: A 127 THR cc_start: 0.9183 (m) cc_final: 0.8887 (m) REVERT: A 131 GLU cc_start: 0.8672 (mt-10) cc_final: 0.7945 (mt-10) REVERT: A 142 ARG cc_start: 0.8523 (ttt90) cc_final: 0.7688 (ttt90) REVERT: A 157 MET cc_start: 0.9146 (tmm) cc_final: 0.8426 (tmm) REVERT: A 196 LEU cc_start: 0.9426 (tp) cc_final: 0.9112 (tp) REVERT: A 275 GLN cc_start: 0.7670 (tp40) cc_final: 0.7311 (tp40) REVERT: A 315 MET cc_start: 0.8889 (ttp) cc_final: 0.8381 (ttp) REVERT: A 397 MET cc_start: 0.6647 (mtm) cc_final: 0.6208 (mtt) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.0629 time to fit residues: 9.1088 Evaluate side-chains 96 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 3 optimal weight: 0.0050 chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 534 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.171588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.149482 restraints weight = 6908.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.154053 restraints weight = 3705.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.157031 restraints weight = 2334.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.159266 restraints weight = 1657.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.160638 restraints weight = 1260.592| |-----------------------------------------------------------------------------| r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3960 Z= 0.127 Angle : 0.606 5.697 5392 Z= 0.303 Chirality : 0.040 0.137 628 Planarity : 0.004 0.048 658 Dihedral : 6.509 92.709 553 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.39), residues: 496 helix: 1.72 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -1.94 (0.58), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 142 TYR 0.016 0.001 TYR A 132 PHE 0.030 0.002 PHE A 149 TRP 0.011 0.001 TRP A 177 HIS 0.002 0.001 HIS A 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 ( 3960) covalent geometry : angle 0.60640 / 0.30 ( 5392) hydrogen bonds : bond 0.04559 / 3.00 ( 288) hydrogen bonds : angle 4.28118 / 3.09 ( 855) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.148 Fit side-chains revert: symmetry clash REVERT: A 63 ASP cc_start: 0.7853 (t0) cc_final: 0.7235 (m-30) REVERT: A 115 HIS cc_start: 0.8279 (m-70) cc_final: 0.7913 (m-70) REVERT: A 127 THR cc_start: 0.8692 (m) cc_final: 0.8456 (m) REVERT: A 130 TYR cc_start: 0.8310 (m-80) cc_final: 0.7890 (m-10) REVERT: A 131 GLU cc_start: 0.8463 (mt-10) cc_final: 0.7767 (mt-10) REVERT: A 142 ARG cc_start: 0.8502 (ttt90) cc_final: 0.7695 (ttt90) REVERT: A 157 MET cc_start: 0.9190 (tmm) cc_final: 0.8462 (tmm) REVERT: A 196 LEU cc_start: 0.9382 (tp) cc_final: 0.9049 (tp) REVERT: A 268 LEU cc_start: 0.7638 (tp) cc_final: 0.7291 (tp) REVERT: A 275 GLN cc_start: 0.7693 (tp40) cc_final: 0.7316 (tp40) REVERT: A 315 MET cc_start: 0.8935 (ttp) cc_final: 0.8455 (ttp) REVERT: A 355 PHE cc_start: 0.8564 (t80) cc_final: 0.8284 (t80) REVERT: A 397 MET cc_start: 0.6702 (mtm) cc_final: 0.6254 (mtt) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.0660 time to fit residues: 9.8979 Evaluate side-chains 97 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 20 optimal weight: 0.3980 chunk 40 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 2 optimal weight: 0.4980 chunk 27 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 6 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 534 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.173801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.150122 restraints weight = 7260.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.154636 restraints weight = 3969.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.158015 restraints weight = 2556.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.160100 restraints weight = 1813.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.161781 restraints weight = 1409.962| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3960 Z= 0.128 Angle : 0.618 6.148 5392 Z= 0.305 Chirality : 0.040 0.126 628 Planarity : 0.004 0.047 658 Dihedral : 6.463 82.615 553 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.39), residues: 496 helix: 1.86 (0.27), residues: 363 sheet: None (None), residues: 0 loop : -1.72 (0.57), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 142 TYR 0.023 0.001 TYR A 99 PHE 0.027 0.002 PHE A 298 TRP 0.011 0.001 TRP A 177 HIS 0.002 0.001 HIS A 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 ( 3960) covalent geometry : angle 0.61830 / 0.31 ( 5392) hydrogen bonds : bond 0.04533 / 2.96 ( 288) hydrogen bonds : angle 4.25859 / 3.07 ( 855) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.082 Fit side-chains REVERT: A 63 ASP cc_start: 0.7842 (t0) cc_final: 0.7219 (m-30) REVERT: A 95 PHE cc_start: 0.7384 (m-80) cc_final: 0.7039 (m-10) REVERT: A 115 HIS cc_start: 0.8276 (m-70) cc_final: 0.7916 (m-70) REVERT: A 127 THR cc_start: 0.8829 (m) cc_final: 0.8552 (m) REVERT: A 130 TYR cc_start: 0.8273 (m-80) cc_final: 0.7850 (m-10) REVERT: A 131 GLU cc_start: 0.8477 (mt-10) cc_final: 0.7806 (mt-10) REVERT: A 142 ARG cc_start: 0.8516 (ttt90) cc_final: 0.7682 (ttt90) REVERT: A 153 MET cc_start: 0.8460 (mmt) cc_final: 0.8125 (tpp) REVERT: A 157 MET cc_start: 0.9143 (tmm) cc_final: 0.8432 (tmm) REVERT: A 196 LEU cc_start: 0.9393 (tp) cc_final: 0.9093 (tp) REVERT: A 315 MET cc_start: 0.8946 (ttp) cc_final: 0.8423 (ttp) REVERT: A 397 MET cc_start: 0.6737 (mtm) cc_final: 0.6286 (mtt) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.0469 time to fit residues: 7.0254 Evaluate side-chains 100 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 17 optimal weight: 0.7980 chunk 30 optimal weight: 0.0070 chunk 7 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 36 optimal weight: 0.0570 chunk 39 optimal weight: 7.9990 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 534 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.172952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.150438 restraints weight = 6974.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.155006 restraints weight = 3707.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.158324 restraints weight = 2345.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.160612 restraints weight = 1637.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.161962 restraints weight = 1238.622| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3960 Z= 0.123 Angle : 0.608 5.884 5392 Z= 0.302 Chirality : 0.039 0.123 628 Planarity : 0.004 0.047 658 Dihedral : 6.435 82.328 553 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.39), residues: 496 helix: 1.72 (0.27), residues: 376 sheet: None (None), residues: 0 loop : -2.30 (0.56), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 142 TYR 0.015 0.001 TYR A 132 PHE 0.027 0.001 PHE A 298 TRP 0.011 0.001 TRP A 177 HIS 0.002 0.000 HIS A 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 ( 3960) covalent geometry : angle 0.60756 / 0.30 ( 5392) hydrogen bonds : bond 0.04431 / 2.93 ( 288) hydrogen bonds : angle 4.25945 / 3.06 ( 855) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 750.07 seconds wall clock time: 13 minutes 35.32 seconds (815.32 seconds total)