Starting phenix.real_space_refine on Thu Jul 2 04:23:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9z2p_73774/07_2026/9z2p_73774.cif Found real_map, /net/cci-nas-00/data/ceres_data/9z2p_73774/07_2026/9z2p_73774.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9z2p_73774/07_2026/9z2p_73774.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9z2p_73774/07_2026/9z2p_73774.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9z2p_73774/07_2026/9z2p_73774.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9z2p_73774/07_2026/9z2p_73774.map" } resolution = 2.91 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 75 5.49 5 S 31 5.16 5 C 3794 2.51 5 N 1116 2.21 5 O 1396 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6412 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4812 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 592, 4790 Classifications: {'peptide': 592} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 551} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 592, 4790 Classifications: {'peptide': 592} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 551} Chain breaks: 1 bond proxies already assigned to first conformer: 4885 Chain: "B" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1600 Classifications: {'RNA': 75} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 31, 'rna3p_pyr': 34} Link IDs: {'rna2p': 10, 'rna3p': 64} Time building chain proxies: 1.97, per 1000 atoms: 0.31 Number of scatterers: 6412 At special positions: 0 Unit cell: (69.864, 98.4, 105.288, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 31 16.00 P 75 15.00 O 1396 8.00 N 1116 7.00 C 3794 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: 0.41 Conformation dependent library (CDL) restraints added in 321.8 milliseconds 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1134 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 8 sheets defined 42.9% alpha, 16.0% beta 23 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 62 through 71 Processing helix chain 'A' and resid 83 through 98 Processing helix chain 'A' and resid 121 through 124 removed outlier: 3.648A pdb=" N GLU A 124 " --> pdb=" O TYR A 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 121 through 124' Processing helix chain 'A' and resid 132 through 139 Processing helix chain 'A' and resid 142 through 156 Processing helix chain 'A' and resid 162 through 165 Processing helix chain 'A' and resid 166 through 173 removed outlier: 3.525A pdb=" N LEU A 170 " --> pdb=" O MET A 166 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASN A 173 " --> pdb=" O PRO A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 199 removed outlier: 3.596A pdb=" N GLN A 193 " --> pdb=" O SER A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 229 Processing helix chain 'A' and resid 242 through 246 removed outlier: 4.002A pdb=" N ILE A 246 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 277 removed outlier: 3.875A pdb=" N MET A 277 " --> pdb=" O ASP A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 289 through 309 removed outlier: 4.783A pdb=" N GLY A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LEU A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 340 removed outlier: 4.236A pdb=" N ALA A 330 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N VAL A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 385 Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.552A pdb=" N PHE A 393 " --> pdb=" O PRO A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 405 removed outlier: 3.858A pdb=" N HIS A 405 " --> pdb=" O LEU A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 408 No H-bonds generated for 'chain 'A' and resid 406 through 408' Processing helix chain 'A' and resid 413 through 418 removed outlier: 4.411A pdb=" N GLN A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 538 removed outlier: 3.816A pdb=" N ILE A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 546 No H-bonds generated for 'chain 'A' and resid 544 through 546' Processing helix chain 'A' and resid 564 through 574 Processing helix chain 'A' and resid 607 through 612 Processing helix chain 'A' and resid 613 through 615 No H-bonds generated for 'chain 'A' and resid 613 through 615' Processing helix chain 'A' and resid 623 through 633 Processing helix chain 'A' and resid 637 through 641 Processing helix chain 'A' and resid 642 through 651 removed outlier: 3.882A pdb=" N ASP A 651 " --> pdb=" O SER A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 702 removed outlier: 3.557A pdb=" N MET A 702 " --> pdb=" O TYR A 698 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 117 Processing sheet with id=AA2, first strand: chain 'A' and resid 106 through 107 Processing sheet with id=AA3, first strand: chain 'A' and resid 343 through 345 Processing sheet with id=AA4, first strand: chain 'A' and resid 343 through 345 removed outlier: 4.337A pdb=" N GLY A 314 " --> pdb=" O LYS A 429 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TYR A 262 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N GLY A 313 " --> pdb=" O TYR A 262 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ARG A 264 " --> pdb=" O GLY A 313 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ARG A 315 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LEU A 266 " --> pdb=" O ARG A 315 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL A 317 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LYS A 179 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N LEU A 266 " --> pdb=" O LYS A 179 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU A 181 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL A 211 " --> pdb=" O MET A 237 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N VAL A 239 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ALA A 213 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N ILE A 236 " --> pdb=" O THR A 583 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N THR A 583 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL A 238 " --> pdb=" O ILE A 581 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 250 through 253 Processing sheet with id=AA6, first strand: chain 'A' and resid 366 through 367 Processing sheet with id=AA7, first strand: chain 'A' and resid 521 through 522 removed outlier: 6.911A pdb=" N LEU A 560 " --> pdb=" O VAL A 587 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 619 through 621 removed outlier: 3.517A pdb=" N ILE A 675 " --> pdb=" O TYR A 661 " (cutoff:3.500A) 187 hydrogen bonds defined for protein. 507 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 61 hydrogen bonds 106 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 1.00 Time building geometry restraints manager: 0.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1698 1.34 - 1.45: 1492 1.45 - 1.57: 3332 1.57 - 1.69: 149 1.69 - 1.81: 50 Bond restraints: 6721 Sorted by residual: bond pdb=" N VAL A 114 " pdb=" CA VAL A 114 " ideal model delta sigma weight residual 1.468 1.459 0.010 1.05e-02 9.07e+03 8.23e-01 bond pdb=" N PRO A 544 " pdb=" CA PRO A 544 " ideal model delta sigma weight residual 1.469 1.480 -0.011 1.28e-02 6.10e+03 7.57e-01 bond pdb=" N3 G B 10 " pdb=" C4 G B 10 " ideal model delta sigma weight residual 1.350 1.344 0.006 7.00e-03 2.04e+04 7.07e-01 bond pdb=" C2 U B 50 " pdb=" N3 U B 50 " ideal model delta sigma weight residual 1.373 1.379 -0.006 7.00e-03 2.04e+04 6.37e-01 bond pdb=" C6 G B 46 " pdb=" N1 G B 46 " ideal model delta sigma weight residual 1.391 1.386 0.005 7.00e-03 2.04e+04 6.10e-01 ... (remaining 6716 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 9310 1.25 - 2.50: 108 2.50 - 3.75: 44 3.75 - 5.00: 4 5.00 - 6.26: 2 Bond angle restraints: 9468 Sorted by residual: angle pdb=" C1' U B 50 " pdb=" N1 U B 50 " pdb=" C2 U B 50 " ideal model delta sigma weight residual 117.70 120.59 -2.89 1.20e+00 6.94e-01 5.80e+00 angle pdb=" C1' C B 11 " pdb=" N1 C B 11 " pdb=" C2 C B 11 " ideal model delta sigma weight residual 118.80 121.42 -2.62 1.10e+00 8.26e-01 5.67e+00 angle pdb=" O2 U B 39 " pdb=" C2 U B 39 " pdb=" N3 U B 39 " ideal model delta sigma weight residual 122.20 120.66 1.54 7.00e-01 2.04e+00 4.84e+00 angle pdb=" N1 C B 56 " pdb=" C2 C B 56 " pdb=" O2 C B 56 " ideal model delta sigma weight residual 118.90 120.18 -1.28 6.00e-01 2.78e+00 4.52e+00 angle pdb=" O4 U B 50 " pdb=" C4 U B 50 " pdb=" C5 U B 50 " ideal model delta sigma weight residual 125.90 124.65 1.25 6.00e-01 2.78e+00 4.35e+00 ... (remaining 9463 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.61: 4048 35.61 - 71.21: 159 71.21 - 106.82: 25 106.82 - 142.42: 1 142.42 - 178.03: 1 Dihedral angle restraints: 4234 sinusoidal: 2488 harmonic: 1746 Sorted by residual: dihedral pdb=" O4' G B 45 " pdb=" C1' G B 45 " pdb=" N9 G B 45 " pdb=" C4 G B 45 " ideal model delta sinusoidal sigma weight residual 254.00 175.44 78.56 1 1.70e+01 3.46e-03 2.66e+01 dihedral pdb=" C4' A B 21 " pdb=" C3' A B 21 " pdb=" O3' A B 21 " pdb=" P G B 22 " ideal model delta sinusoidal sigma weight residual 220.00 41.97 178.03 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" O4' G B 15 " pdb=" C1' G B 15 " pdb=" N9 G B 15 " pdb=" C4 G B 15 " ideal model delta sinusoidal sigma weight residual -90.00 -38.34 -51.66 1 2.00e+01 2.50e-03 9.11e+00 ... (remaining 4231 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 720 0.026 - 0.051: 244 0.051 - 0.076: 72 0.076 - 0.102: 33 0.102 - 0.127: 34 Chirality restraints: 1103 Sorted by residual: chirality pdb=" CA VAL A 58 " pdb=" N VAL A 58 " pdb=" C VAL A 58 " pdb=" CB VAL A 58 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA ILE A 523 " pdb=" N ILE A 523 " pdb=" C ILE A 523 " pdb=" CB ILE A 523 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.49e-01 chirality pdb=" CA VAL A 690 " pdb=" N VAL A 690 " pdb=" C VAL A 690 " pdb=" CB VAL A 690 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.48e-01 ... (remaining 1100 not shown) Planarity restraints: 934 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 531 " 0.025 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO A 532 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 532 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 532 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 167 " -0.021 5.00e-02 4.00e+02 3.16e-02 1.59e+00 pdb=" N PRO A 168 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 168 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 168 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 540 " 0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO A 541 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 541 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 541 " 0.017 5.00e-02 4.00e+02 ... (remaining 931 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1076 2.77 - 3.30: 5727 3.30 - 3.83: 11125 3.83 - 4.37: 12943 4.37 - 4.90: 20724 Nonbonded interactions: 51595 Sorted by model distance: nonbonded pdb=" OH TYR A 52 " pdb=" OD2 ASP A 274 " model vdw 2.233 3.040 nonbonded pdb=" O2' A B 21 " pdb=" OP1 G B 22 " model vdw 2.242 3.040 nonbonded pdb=" O GLU A 525 " pdb=" NH1 ARG A 545 " model vdw 2.268 3.120 nonbonded pdb=" OG1 THR A 368 " pdb=" OD1 ASP A 370 " model vdw 2.302 3.040 nonbonded pdb=" O PRO A 270 " pdb=" NE2 GLN A 299 " model vdw 2.339 3.120 ... (remaining 51590 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.44 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.820 Find NCS groups from input model: 0.030 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:6.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 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 6721 Z= 0.135 Angle : 0.424 6.256 9468 Z= 0.272 Chirality : 0.035 0.127 1103 Planarity : 0.004 0.037 934 Dihedral : 16.552 178.031 3100 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.56 % Allowed : 2.42 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.48 (0.35), residues: 591 helix: 1.98 (0.39), residues: 201 sheet: -0.20 (0.54), residues: 93 loop : 0.85 (0.36), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 315 TYR 0.010 0.001 TYR A 51 PHE 0.010 0.001 PHE A 66 TRP 0.007 0.001 TRP A 287 HIS 0.002 0.000 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 ( 6721) covalent geometry : angle 0.42442 / 0.27 ( 9468) hydrogen bonds : bond 0.14341 / 9.27 ( 246) hydrogen bonds : angle 5.90862 / 4.41 ( 613) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.133 Fit side-chains revert: symmetry clash REVERT: A 175 ARG cc_start: 0.8181 (mmt180) cc_final: 0.7739 (mmm-85) REVERT: A 433 MET cc_start: 0.9266 (mmt) cc_final: 0.8908 (mmt) REVERT: A 436 ASN cc_start: 0.8127 (t0) cc_final: 0.7530 (p0) REVERT: A 651 ASP cc_start: 0.9096 (m-30) cc_final: 0.8826 (p0) outliers start: 3 outliers final: 2 residues processed: 62 average time/residue: 0.6877 time to fit residues: 44.1605 Evaluate side-chains 35 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 693 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.121825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.065419 restraints weight = 20872.830| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 3.58 r_work: 0.2599 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2596 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2596 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6721 Z= 0.176 Angle : 0.520 7.565 9468 Z= 0.270 Chirality : 0.039 0.136 1103 Planarity : 0.005 0.050 934 Dihedral : 19.817 175.948 1853 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.30 % Allowed : 7.99 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.40 (0.35), residues: 591 helix: 1.95 (0.38), residues: 202 sheet: -0.48 (0.52), residues: 91 loop : 0.86 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 256 TYR 0.013 0.001 TYR A 52 PHE 0.014 0.002 PHE A 543 TRP 0.008 0.001 TRP A 680 HIS 0.002 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 ( 6721) covalent geometry : angle 0.51982 / 0.27 ( 9468) hydrogen bonds : bond 0.04407 / 2.91 ( 246) hydrogen bonds : angle 4.66068 / 3.45 ( 613) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: A 175 ARG cc_start: 0.8173 (mmt180) cc_final: 0.7720 (mmm-85) REVERT: A 433 MET cc_start: 0.9275 (mmt) cc_final: 0.8792 (mmt) REVERT: A 436 ASN cc_start: 0.8162 (t0) cc_final: 0.7473 (p0) REVERT: A 651 ASP cc_start: 0.9097 (m-30) cc_final: 0.8805 (p0) outliers start: 7 outliers final: 2 residues processed: 37 average time/residue: 0.5433 time to fit residues: 21.2939 Evaluate side-chains 32 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 578 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 56 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 15 optimal weight: 0.0970 chunk 34 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 1 optimal weight: 0.4980 chunk 49 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.122778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.065214 restraints weight = 38376.096| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 4.46 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2802 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2802 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6721 Z= 0.103 Angle : 0.442 6.748 9468 Z= 0.228 Chirality : 0.036 0.131 1103 Planarity : 0.004 0.039 934 Dihedral : 19.776 174.210 1851 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.93 % Allowed : 8.36 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 (0.35), residues: 591 helix: 2.00 (0.38), residues: 202 sheet: -0.53 (0.51), residues: 96 loop : 0.90 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 256 TYR 0.008 0.001 TYR A 52 PHE 0.012 0.001 PHE A 543 TRP 0.007 0.001 TRP A 287 HIS 0.002 0.000 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.10 ( 6721) covalent geometry : angle 0.44241 / 0.23 ( 9468) hydrogen bonds : bond 0.03711 / 2.50 ( 246) hydrogen bonds : angle 4.36864 / 3.25 ( 613) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: A 175 ARG cc_start: 0.7939 (mmt180) cc_final: 0.7541 (mmm-85) REVERT: A 651 ASP cc_start: 0.9063 (m-30) cc_final: 0.8829 (p0) outliers start: 5 outliers final: 1 residues processed: 33 average time/residue: 0.6098 time to fit residues: 21.1377 Evaluate side-chains 28 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 2 optimal weight: 0.0170 chunk 52 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 53 optimal weight: 0.0370 chunk 30 optimal weight: 3.9990 chunk 16 optimal weight: 0.0070 chunk 14 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 overall best weight: 0.3914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 569 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.123695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.066504 restraints weight = 34070.434| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 4.36 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2818 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2818 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6721 Z= 0.087 Angle : 0.420 6.949 9468 Z= 0.216 Chirality : 0.036 0.135 1103 Planarity : 0.004 0.039 934 Dihedral : 19.709 173.117 1851 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.74 % Allowed : 9.29 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.50 (0.35), residues: 591 helix: 2.04 (0.38), residues: 203 sheet: -0.47 (0.52), residues: 96 loop : 0.95 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 256 TYR 0.010 0.001 TYR A 52 PHE 0.010 0.001 PHE A 48 TRP 0.010 0.001 TRP A 435 HIS 0.002 0.000 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.09 ( 6721) covalent geometry : angle 0.41991 / 0.22 ( 9468) hydrogen bonds : bond 0.03273 / 2.24 ( 246) hydrogen bonds : angle 4.11028 / 3.04 ( 613) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: A 175 ARG cc_start: 0.7878 (mmt180) cc_final: 0.7494 (tpp80) REVERT: A 651 ASP cc_start: 0.9028 (m-30) cc_final: 0.8792 (p0) outliers start: 4 outliers final: 1 residues processed: 34 average time/residue: 0.6124 time to fit residues: 21.9387 Evaluate side-chains 30 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 60 optimal weight: 20.0000 chunk 13 optimal weight: 0.0980 chunk 48 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.122716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.066430 restraints weight = 26254.705| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 3.94 r_work: 0.2612 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2607 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2607 r_free = 0.2607 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2607 r_free = 0.2607 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2607 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6721 Z= 0.110 Angle : 0.434 6.855 9468 Z= 0.222 Chirality : 0.036 0.138 1103 Planarity : 0.004 0.040 934 Dihedral : 19.688 172.891 1851 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.93 % Allowed : 9.29 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.48 (0.35), residues: 591 helix: 2.04 (0.38), residues: 203 sheet: -0.41 (0.52), residues: 96 loop : 0.89 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 639 TYR 0.009 0.001 TYR A 52 PHE 0.010 0.001 PHE A 637 TRP 0.008 0.001 TRP A 435 HIS 0.001 0.000 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 ( 6721) covalent geometry : angle 0.43436 / 0.22 ( 9468) hydrogen bonds : bond 0.03389 / 2.30 ( 246) hydrogen bonds : angle 4.11551 / 3.05 ( 613) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: A 175 ARG cc_start: 0.8192 (mmt180) cc_final: 0.7725 (tpp80) REVERT: A 316 MET cc_start: 0.9392 (ttp) cc_final: 0.9130 (ttt) REVERT: A 651 ASP cc_start: 0.9104 (m-30) cc_final: 0.8788 (p0) outliers start: 5 outliers final: 2 residues processed: 33 average time/residue: 0.6693 time to fit residues: 23.2454 Evaluate side-chains 32 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 211 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 41 optimal weight: 0.0060 chunk 50 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 42 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.123844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.066938 restraints weight = 29681.345| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 4.16 r_work: 0.2614 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2606 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2606 r_free = 0.2606 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2606 r_free = 0.2606 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2606 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6721 Z= 0.087 Angle : 0.424 7.366 9468 Z= 0.217 Chirality : 0.036 0.143 1103 Planarity : 0.004 0.039 934 Dihedral : 19.674 172.444 1851 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.93 % Allowed : 9.85 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.55 (0.35), residues: 591 helix: 2.09 (0.38), residues: 203 sheet: -0.38 (0.53), residues: 96 loop : 0.95 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 639 TYR 0.010 0.001 TYR A 52 PHE 0.011 0.001 PHE A 48 TRP 0.006 0.001 TRP A 284 HIS 0.001 0.000 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.09 ( 6721) covalent geometry : angle 0.42358 / 0.22 ( 9468) hydrogen bonds : bond 0.03193 / 2.17 ( 246) hydrogen bonds : angle 4.02752 / 2.97 ( 613) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.167 Fit side-chains revert: symmetry clash REVERT: A 175 ARG cc_start: 0.8098 (mmt180) cc_final: 0.7622 (tpp80) REVERT: A 651 ASP cc_start: 0.9099 (m-30) cc_final: 0.8781 (p0) outliers start: 5 outliers final: 2 residues processed: 32 average time/residue: 0.5942 time to fit residues: 20.0925 Evaluate side-chains 31 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 29 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 211 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 0 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 19 optimal weight: 0.0000 chunk 12 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 20.0000 chunk 7 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.122167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.065239 restraints weight = 24912.256| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 3.89 r_work: 0.2587 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2588 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2588 r_free = 0.2588 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2588 r_free = 0.2588 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2588 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6721 Z= 0.140 Angle : 0.454 7.627 9468 Z= 0.233 Chirality : 0.037 0.145 1103 Planarity : 0.004 0.040 934 Dihedral : 19.658 172.430 1851 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.56 % Allowed : 10.22 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.49 (0.35), residues: 591 helix: 2.04 (0.38), residues: 203 sheet: -0.41 (0.52), residues: 96 loop : 0.91 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 639 TYR 0.009 0.001 TYR A 52 PHE 0.009 0.001 PHE A 48 TRP 0.008 0.001 TRP A 287 HIS 0.002 0.000 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 ( 6721) covalent geometry : angle 0.45368 / 0.23 ( 9468) hydrogen bonds : bond 0.03578 / 2.41 ( 246) hydrogen bonds : angle 4.11239 / 3.04 ( 613) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: A 175 ARG cc_start: 0.8185 (mmt180) cc_final: 0.7683 (tpp80) REVERT: A 651 ASP cc_start: 0.9074 (m-30) cc_final: 0.8750 (p0) outliers start: 3 outliers final: 2 residues processed: 33 average time/residue: 0.6646 time to fit residues: 23.0405 Evaluate side-chains 33 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 211 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 6 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 53 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 64 optimal weight: 20.0000 chunk 62 optimal weight: 20.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.122710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.066131 restraints weight = 23644.082| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 3.76 r_work: 0.2613 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2609 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2609 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6721 Z= 0.107 Angle : 0.444 8.422 9468 Z= 0.228 Chirality : 0.036 0.148 1103 Planarity : 0.004 0.039 934 Dihedral : 19.676 172.160 1851 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.56 % Allowed : 10.59 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.50 (0.35), residues: 591 helix: 2.07 (0.38), residues: 203 sheet: -0.41 (0.53), residues: 96 loop : 0.91 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 639 TYR 0.009 0.001 TYR A 52 PHE 0.011 0.001 PHE A 48 TRP 0.007 0.001 TRP A 287 HIS 0.002 0.000 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 6721) covalent geometry : angle 0.44361 / 0.23 ( 9468) hydrogen bonds : bond 0.03350 / 2.26 ( 246) hydrogen bonds : angle 4.05426 / 2.98 ( 613) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: A 175 ARG cc_start: 0.8219 (mmt180) cc_final: 0.7731 (tpp80) REVERT: A 639 ARG cc_start: 0.8796 (ppt170) cc_final: 0.8570 (ppt170) REVERT: A 651 ASP cc_start: 0.9057 (m-30) cc_final: 0.8748 (p0) outliers start: 3 outliers final: 2 residues processed: 34 average time/residue: 0.6098 time to fit residues: 21.8490 Evaluate side-chains 33 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 211 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 41 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 10.0000 chunk 60 optimal weight: 30.0000 chunk 19 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.122757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.065438 restraints weight = 37389.313| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 4.46 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2804 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2804 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6721 Z= 0.108 Angle : 0.437 8.009 9468 Z= 0.225 Chirality : 0.036 0.152 1103 Planarity : 0.004 0.039 934 Dihedral : 19.664 172.083 1851 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.74 % Allowed : 10.22 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.53 (0.35), residues: 591 helix: 2.05 (0.38), residues: 203 sheet: -0.45 (0.51), residues: 104 loop : 1.03 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 558 TYR 0.010 0.001 TYR A 52 PHE 0.011 0.001 PHE A 48 TRP 0.007 0.001 TRP A 287 HIS 0.002 0.000 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 6721) covalent geometry : angle 0.43689 / 0.23 ( 9468) hydrogen bonds : bond 0.03304 / 2.23 ( 246) hydrogen bonds : angle 4.03377 / 2.97 ( 613) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.169 Fit side-chains revert: symmetry clash REVERT: A 175 ARG cc_start: 0.7929 (mmt180) cc_final: 0.7505 (tpp80) REVERT: A 651 ASP cc_start: 0.9021 (m-30) cc_final: 0.8761 (p0) REVERT: A 672 GLN cc_start: 0.7999 (mp10) cc_final: 0.7767 (mm-40) outliers start: 4 outliers final: 2 residues processed: 36 average time/residue: 0.6372 time to fit residues: 24.1341 Evaluate side-chains 32 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 211 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 44 optimal weight: 0.0170 chunk 9 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 0.0980 chunk 57 optimal weight: 0.0370 chunk 65 optimal weight: 10.0000 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.123323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.066913 restraints weight = 27305.953| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 4.02 r_work: 0.2620 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2618 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2618 r_free = 0.2618 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2618 r_free = 0.2618 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2618 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6721 Z= 0.083 Angle : 0.440 7.441 9468 Z= 0.227 Chirality : 0.036 0.153 1103 Planarity : 0.004 0.039 934 Dihedral : 19.668 171.903 1851 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.37 % Allowed : 11.15 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.55 (0.36), residues: 591 helix: 2.05 (0.38), residues: 203 sheet: -0.40 (0.52), residues: 104 loop : 1.04 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 639 TYR 0.009 0.001 TYR A 52 PHE 0.010 0.001 PHE A 48 TRP 0.011 0.001 TRP A 284 HIS 0.002 0.000 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00185 / 0.08 ( 6721) covalent geometry : angle 0.44032 / 0.23 ( 9468) hydrogen bonds : bond 0.03102 / 2.09 ( 246) hydrogen bonds : angle 3.96693 / 2.93 ( 613) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.182 Fit side-chains revert: symmetry clash REVERT: A 175 ARG cc_start: 0.8145 (mmt180) cc_final: 0.7671 (tpp80) REVERT: A 651 ASP cc_start: 0.9057 (m-30) cc_final: 0.8745 (p0) REVERT: A 672 GLN cc_start: 0.8135 (mp10) cc_final: 0.7901 (mm-40) outliers start: 2 outliers final: 2 residues processed: 32 average time/residue: 0.6677 time to fit residues: 22.5187 Evaluate side-chains 31 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 29 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 211 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 32 optimal weight: 0.0970 chunk 56 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 22 optimal weight: 0.3980 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 0.0070 chunk 12 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.123457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.067121 restraints weight = 27800.785| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 4.04 r_work: 0.2624 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2614 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2614 r_free = 0.2614 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2614 r_free = 0.2614 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2614 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6721 Z= 0.085 Angle : 0.444 7.215 9468 Z= 0.228 Chirality : 0.036 0.154 1103 Planarity : 0.004 0.039 934 Dihedral : 19.652 171.833 1851 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.37 % Allowed : 10.78 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.59 (0.36), residues: 591 helix: 2.07 (0.38), residues: 203 sheet: -0.43 (0.51), residues: 104 loop : 1.09 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 639 TYR 0.010 0.001 TYR A 52 PHE 0.010 0.001 PHE A 638 TRP 0.011 0.001 TRP A 284 HIS 0.002 0.000 HIS A 405 Details of bonding type rmsd/Z covalent geometry : bond 0.00194 / 0.08 ( 6721) covalent geometry : angle 0.44448 / 0.23 ( 9468) hydrogen bonds : bond 0.03052 / 2.06 ( 246) hydrogen bonds : angle 3.89409 / 2.88 ( 613) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2203.69 seconds wall clock time: 38 minutes 19.05 seconds (2299.05 seconds total)