Starting phenix.real_space_refine on Thu Jul 2 22:48:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zpb_60331/07_2026/8zpb_60331_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zpb_60331/07_2026/8zpb_60331.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zpb_60331/07_2026/8zpb_60331.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zpb_60331/07_2026/8zpb_60331.map" model { file = "/net/cci-nas-00/data/ceres_data/8zpb_60331/07_2026/8zpb_60331_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zpb_60331/07_2026/8zpb_60331_trim.cif" } resolution = 2.6 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= 0.024 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: 8 Type Number sf(0) Gaussians P 1 5.49 5 S 24 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 3560 2.51 5 N 845 2.21 5 O 986 1.98 5 H 5257 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s 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: 10676 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 8801 Classifications: {'peptide': 551} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 530} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 1779 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain breaks: 1 Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 90 Ad-hoc single atom residues: {' NA': 2, ' CL': 1} Unusual residues: {'LNR': 1, 'PTY': 1} Classifications: {'undetermined': 2, 'water': 51} Link IDs: {None: 51} Chain breaks: 3 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 1.83, per 1000 atoms: 0.17 Number of scatterers: 10676 At special positions: 0 Unit cell: (98.44, 74.52, 79.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Cl 1 17.00 S 24 16.00 P 1 15.00 Na 2 11.00 O 986 8.00 N 845 7.00 C 3560 6.00 H 5257 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 185 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 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: 0.95 Conformation dependent library (CDL) restraints added in 265.7 milliseconds 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1224 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 5 sheets defined 69.7% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 61 through 74 removed outlier: 3.631A pdb=" N PHE A 65 " --> pdb=" O LYS A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 81 Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 121 removed outlier: 3.972A pdb=" N LEU A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) Proline residue: A 97 - end of helix removed outlier: 4.825A pdb=" N MET A 107 " --> pdb=" O ILE A 103 " (cutoff:3.500A) Proline residue: A 108 - end of helix Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 134 through 166 removed outlier: 3.771A pdb=" N GLY A 138 " --> pdb=" O PHE A 134 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N TYR A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N VAL A 154 " --> pdb=" O PHE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 234 through 253 Processing helix chain 'A' and resid 255 through 267 removed outlier: 4.207A pdb=" N SER A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TRP A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ILE A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 282 removed outlier: 3.804A pdb=" N PHE A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 296 removed outlier: 3.631A pdb=" N GLY A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 304 through 320 removed outlier: 4.205A pdb=" N TRP A 308 " --> pdb=" O GLU A 304 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 338 through 372 Processing helix chain 'A' and resid 375 through 379 Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'A' and resid 389 through 397 Processing helix chain 'A' and resid 400 through 435 removed outlier: 3.820A pdb=" N ASP A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 441 Processing helix chain 'A' and resid 441 through 458 Processing helix chain 'A' and resid 459 through 462 removed outlier: 3.688A pdb=" N THR A 462 " --> pdb=" O PHE A 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 459 through 462' Processing helix chain 'A' and resid 464 through 476 removed outlier: 3.580A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 494 Processing helix chain 'A' and resid 497 through 510 Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 551 through 567 removed outlier: 3.555A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 580 Processing helix chain 'A' and resid 583 through 593 Processing helix chain 'A' and resid 594 through 597 Processing helix chain 'A' and resid 598 through 604 removed outlier: 4.399A pdb=" N ALA A 602 " --> pdb=" O HIS A 598 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN A 603 " --> pdb=" O HIS A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 609 Processing helix chain 'A' and resid 610 through 615 removed outlier: 4.037A pdb=" N TRP A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 57 removed outlier: 3.912A pdb=" N ARG A 56 " --> pdb=" O GLN B 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 544 through 545 Processing sheet with id=AA3, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.692A pdb=" N MET B 34 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ALA B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 13 340 hydrogen bonds defined for protein. 951 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.51 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5250 1.03 - 1.23: 20 1.23 - 1.42: 2447 1.42 - 1.62: 3026 1.62 - 1.81: 39 Bond restraints: 10782 Sorted by residual: bond pdb=" CAE LNR A 701 " pdb=" CAI LNR A 701 " ideal model delta sigma weight residual 1.384 1.524 -0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" CAG LNR A 701 " pdb=" CAJ LNR A 701 " ideal model delta sigma weight residual 1.384 1.524 -0.140 2.00e-02 2.50e+03 4.91e+01 bond pdb=" CAF LNR A 701 " pdb=" CAK LNR A 701 " ideal model delta sigma weight residual 1.386 1.524 -0.138 2.00e-02 2.50e+03 4.76e+01 bond pdb=" CAI LNR A 701 " pdb=" CAJ LNR A 701 " ideal model delta sigma weight residual 1.402 1.317 0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" CAG LNR A 701 " pdb=" CAK LNR A 701 " ideal model delta sigma weight residual 1.395 1.316 0.079 2.00e-02 2.50e+03 1.55e+01 ... (remaining 10777 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 18221 1.14 - 2.28: 1067 2.28 - 3.42: 70 3.42 - 4.57: 19 4.57 - 5.71: 3 Bond angle restraints: 19380 Sorted by residual: angle pdb=" N MET A 107 " pdb=" CA MET A 107 " pdb=" C MET A 107 " ideal model delta sigma weight residual 112.75 108.87 3.88 1.36e+00 5.41e-01 8.15e+00 angle pdb=" CA SER A 182 " pdb=" C SER A 182 " pdb=" O SER A 182 " ideal model delta sigma weight residual 121.01 117.76 3.25 1.18e+00 7.18e-01 7.61e+00 angle pdb=" N PRO A 183 " pdb=" CA PRO A 183 " pdb=" C PRO A 183 " ideal model delta sigma weight residual 114.35 110.97 3.38 1.25e+00 6.40e-01 7.31e+00 angle pdb=" CA TRP A 80 " pdb=" C TRP A 80 " pdb=" O TRP A 80 " ideal model delta sigma weight residual 119.41 116.41 3.00 1.13e+00 7.83e-01 7.07e+00 angle pdb=" CA SER A 182 " pdb=" C SER A 182 " pdb=" N PRO A 183 " ideal model delta sigma weight residual 117.60 120.69 -3.09 1.18e+00 7.18e-01 6.85e+00 ... (remaining 19375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.82: 4766 23.82 - 47.64: 267 47.64 - 71.46: 85 71.46 - 95.28: 2 95.28 - 119.11: 1 Dihedral angle restraints: 5121 sinusoidal: 2620 harmonic: 2501 Sorted by residual: dihedral pdb=" N1 PTY A 705 " pdb=" C2 PTY A 705 " pdb=" C3 PTY A 705 " pdb=" O11 PTY A 705 " ideal model delta sinusoidal sigma weight residual 65.33 -175.56 -119.11 1 3.00e+01 1.11e-03 1.59e+01 dihedral pdb=" CA ILE B 51 " pdb=" C ILE B 51 " pdb=" N GLN B 52 " pdb=" CA GLN B 52 " ideal model delta harmonic sigma weight residual -180.00 -162.11 -17.89 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA TRP A 128 " pdb=" C TRP A 128 " pdb=" N LYS A 129 " pdb=" CA LYS A 129 " ideal model delta harmonic sigma weight residual 180.00 164.13 15.87 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 5118 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 665 0.046 - 0.091: 129 0.091 - 0.137: 30 0.137 - 0.182: 1 0.182 - 0.228: 1 Chirality restraints: 826 Sorted by residual: chirality pdb=" CAL LNR A 701 " pdb=" CAH LNR A 701 " pdb=" CAK LNR A 701 " pdb=" OAD LNR A 701 " both_signs ideal model delta sigma weight residual False -2.28 -2.51 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA VAL A 79 " pdb=" N VAL A 79 " pdb=" C VAL A 79 " pdb=" CB VAL A 79 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.64e-01 chirality pdb=" CA VAL B 2 " pdb=" N VAL B 2 " pdb=" C VAL B 2 " pdb=" CB VAL B 2 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 823 not shown) Planarity restraints: 1563 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 102 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.09e+00 pdb=" C LEU A 102 " 0.035 2.00e-02 2.50e+03 pdb=" O LEU A 102 " -0.013 2.00e-02 2.50e+03 pdb=" N ILE A 103 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 213 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.33e+00 pdb=" C PHE A 213 " -0.026 2.00e-02 2.50e+03 pdb=" O PHE A 213 " 0.010 2.00e-02 2.50e+03 pdb=" N TYR A 214 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 391 " -0.023 5.00e-02 4.00e+02 3.51e-02 1.98e+00 pdb=" N PRO A 392 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 392 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 392 " -0.020 5.00e-02 4.00e+02 ... (remaining 1560 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 629 2.19 - 2.79: 21815 2.79 - 3.39: 32592 3.39 - 4.00: 43958 4.00 - 4.60: 68263 Nonbonded interactions: 167257 Sorted by model distance: nonbonded pdb=" O GLN B 52 " pdb="HH22 ARG B 71 " model vdw 1.582 2.450 nonbonded pdb=" OE2 GLU B 6 " pdb=" H CYS B 95 " model vdw 1.602 2.450 nonbonded pdb=" O PHE A 495 " pdb="HE21 GLN A 608 " model vdw 1.609 2.450 nonbonded pdb=" OE1 GLU B 6 " pdb=" H GLY B 113 " model vdw 1.655 2.450 nonbonded pdb="HH22 ARG A 81 " pdb=" O HOH A 810 " model vdw 1.663 2.450 ... (remaining 167252 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.110 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: 0.080 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.950 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 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 0.140 5527 Z= 0.261 Angle : 0.563 5.707 7530 Z= 0.328 Chirality : 0.039 0.228 826 Planarity : 0.004 0.051 922 Dihedral : 15.800 119.105 1882 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.08 % Allowed : 14.52 % Favored : 84.41 % 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: 0.89 (0.33), residues: 659 helix: 1.10 (0.27), residues: 389 sheet: -1.46 (0.86), residues: 33 loop : 0.24 (0.41), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 301 TYR 0.015 0.002 TYR A 572 PHE 0.014 0.001 PHE A 409 TRP 0.015 0.001 TRP A 556 HIS 0.002 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.26 ( 5525) covalent geometry : angle 0.56311 / 0.33 ( 7526) SS BOND : bond 0.00235 / 0.12 ( 2) SS BOND : angle 0.68477 / 0.40 ( 4) hydrogen bonds : bond 0.12741 / 7.99 ( 334) hydrogen bonds : angle 6.00121 / 4.23 ( 951) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 204 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 TRP cc_start: 0.8521 (OUTLIER) cc_final: 0.7750 (t60) REVERT: A 121 ARG cc_start: 0.8502 (mtm180) cc_final: 0.7511 (mtp180) outliers start: 6 outliers final: 4 residues processed: 90 average time/residue: 0.8685 time to fit residues: 82.9713 Evaluate side-chains 88 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TRP Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 610 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.2980 chunk 27 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 = 0.3457 r_free = 0.3457 target = 0.131986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.114245 restraints weight = 15306.165| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.08 r_work: 0.3562 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.0841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5527 Z= 0.216 Angle : 0.552 5.604 7530 Z= 0.301 Chirality : 0.040 0.134 826 Planarity : 0.005 0.063 922 Dihedral : 8.388 78.107 757 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.79 % Allowed : 13.80 % Favored : 84.41 % 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: 0.98 (0.33), residues: 659 helix: 1.01 (0.26), residues: 389 sheet: -1.77 (0.71), residues: 33 loop : 0.66 (0.43), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 71 TYR 0.016 0.002 TYR A 87 PHE 0.017 0.002 PHE A 409 TRP 0.009 0.001 TRP A 235 HIS 0.004 0.001 HIS A 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.22 ( 5525) covalent geometry : angle 0.55154 / 0.30 ( 7526) SS BOND : bond 0.00317 / 0.17 ( 2) SS BOND : angle 1.28488 / 0.74 ( 4) hydrogen bonds : bond 0.04849 / 3.04 ( 334) hydrogen bonds : angle 5.39600 / 3.91 ( 951) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 204 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: A 80 TRP cc_start: 0.8418 (OUTLIER) cc_final: 0.7583 (t60) REVERT: A 121 ARG cc_start: 0.8409 (mtm180) cc_final: 0.7603 (mtp180) REVERT: A 206 LYS cc_start: 0.7460 (OUTLIER) cc_final: 0.6802 (tttt) REVERT: A 341 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7239 (ptm-80) REVERT: A 509 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.7931 (mtt) REVERT: A 612 GLN cc_start: 0.7757 (mp-120) cc_final: 0.7528 (pm20) outliers start: 10 outliers final: 5 residues processed: 90 average time/residue: 0.9319 time to fit residues: 89.0115 Evaluate side-chains 94 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TRP Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 610 GLN Chi-restraints excluded: chain B residue 25 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3557 r_free = 0.3557 target = 0.138709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.121711 restraints weight = 15232.945| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 1.08 r_work: 0.3581 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5527 Z= 0.162 Angle : 0.509 5.438 7530 Z= 0.277 Chirality : 0.038 0.130 826 Planarity : 0.004 0.045 922 Dihedral : 7.609 68.878 756 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.15 % Allowed : 13.44 % Favored : 84.41 % 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: 1.16 (0.33), residues: 659 helix: 1.18 (0.27), residues: 385 sheet: -1.76 (0.69), residues: 33 loop : 0.70 (0.44), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 301 TYR 0.015 0.002 TYR A 87 PHE 0.016 0.001 PHE A 316 TRP 0.009 0.001 TRP A 235 HIS 0.003 0.001 HIS A 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 ( 5525) covalent geometry : angle 0.50854 / 0.28 ( 7526) SS BOND : bond 0.00253 / 0.13 ( 2) SS BOND : angle 0.97867 / 0.57 ( 4) hydrogen bonds : bond 0.04344 / 2.73 ( 334) hydrogen bonds : angle 5.15994 / 3.74 ( 951) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 204 is missing expected H atoms. Skipping. Evaluate side-chains 95 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: A 80 TRP cc_start: 0.8375 (OUTLIER) cc_final: 0.7601 (t60) REVERT: A 121 ARG cc_start: 0.8390 (mtm180) cc_final: 0.7559 (mtp180) REVERT: A 206 LYS cc_start: 0.7478 (OUTLIER) cc_final: 0.6809 (tttt) REVERT: A 341 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7225 (ptm-80) REVERT: A 509 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.7739 (mtm) REVERT: B 115 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.7504 (tm-30) outliers start: 12 outliers final: 5 residues processed: 89 average time/residue: 0.9624 time to fit residues: 90.8768 Evaluate side-chains 91 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TRP Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 610 GLN Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 115 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 24 optimal weight: 1.9990 chunk 2 optimal weight: 0.2980 chunk 6 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.129782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.111334 restraints weight = 14704.012| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.18 r_work: 0.3054 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5527 Z= 0.160 Angle : 0.502 5.382 7530 Z= 0.272 Chirality : 0.038 0.127 826 Planarity : 0.004 0.045 922 Dihedral : 7.151 66.805 755 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.15 % Allowed : 13.08 % Favored : 84.77 % 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: 1.23 (0.33), residues: 659 helix: 1.23 (0.27), residues: 385 sheet: -1.69 (0.68), residues: 33 loop : 0.75 (0.44), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 301 TYR 0.015 0.002 TYR A 87 PHE 0.015 0.001 PHE A 316 TRP 0.009 0.001 TRP A 59 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 ( 5525) covalent geometry : angle 0.50122 / 0.27 ( 7526) SS BOND : bond 0.00255 / 0.13 ( 2) SS BOND : angle 0.97864 / 0.56 ( 4) hydrogen bonds : bond 0.04243 / 2.67 ( 334) hydrogen bonds : angle 5.09627 / 3.70 ( 951) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 204 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 80 TRP cc_start: 0.8376 (OUTLIER) cc_final: 0.7590 (t60) REVERT: A 121 ARG cc_start: 0.8356 (mtm180) cc_final: 0.7292 (mtp180) REVERT: A 206 LYS cc_start: 0.7511 (OUTLIER) cc_final: 0.6714 (tttt) REVERT: A 341 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.7105 (ptm-80) REVERT: A 359 PHE cc_start: 0.8225 (OUTLIER) cc_final: 0.7902 (m-80) REVERT: A 378 ASP cc_start: 0.8160 (m-30) cc_final: 0.7949 (m-30) REVERT: B 56 ARG cc_start: 0.8383 (tmm-80) cc_final: 0.8046 (ttp80) REVERT: B 115 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.7162 (tm-30) outliers start: 12 outliers final: 4 residues processed: 86 average time/residue: 0.9465 time to fit residues: 86.1459 Evaluate side-chains 88 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TRP Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 115 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 50 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.128076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.110015 restraints weight = 14553.602| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.12 r_work: 0.3054 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5527 Z= 0.182 Angle : 0.514 5.340 7530 Z= 0.279 Chirality : 0.038 0.128 826 Planarity : 0.004 0.046 922 Dihedral : 6.562 66.898 752 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.15 % Allowed : 13.62 % Favored : 84.23 % 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: 1.19 (0.33), residues: 659 helix: 1.19 (0.27), residues: 385 sheet: -1.64 (0.68), residues: 33 loop : 0.75 (0.44), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 301 TYR 0.016 0.002 TYR A 87 PHE 0.016 0.001 PHE A 316 TRP 0.009 0.001 TRP A 59 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 ( 5525) covalent geometry : angle 0.51354 / 0.28 ( 7526) SS BOND : bond 0.00291 / 0.15 ( 2) SS BOND : angle 1.12517 / 0.64 ( 4) hydrogen bonds : bond 0.04399 / 2.77 ( 334) hydrogen bonds : angle 5.16769 / 3.75 ( 951) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 204 is missing expected H atoms. Skipping. Evaluate side-chains 95 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 80 TRP cc_start: 0.8404 (OUTLIER) cc_final: 0.7600 (t60) REVERT: A 121 ARG cc_start: 0.8323 (mtm180) cc_final: 0.7262 (mtp180) REVERT: A 206 LYS cc_start: 0.7491 (OUTLIER) cc_final: 0.6665 (tttt) REVERT: A 304 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7584 (mm-30) REVERT: A 359 PHE cc_start: 0.8227 (OUTLIER) cc_final: 0.7911 (m-80) REVERT: B 56 ARG cc_start: 0.8427 (tmm-80) cc_final: 0.8086 (ttp80) REVERT: B 115 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.7097 (tm-30) outliers start: 12 outliers final: 5 residues processed: 89 average time/residue: 0.9628 time to fit residues: 90.6636 Evaluate side-chains 90 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TRP Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 115 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 48 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 3 optimal weight: 0.4980 chunk 15 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3395 r_free = 0.3395 target = 0.129931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.111616 restraints weight = 14715.841| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.17 r_work: 0.3057 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5527 Z= 0.158 Angle : 0.496 5.281 7530 Z= 0.268 Chirality : 0.037 0.126 826 Planarity : 0.004 0.046 922 Dihedral : 6.398 67.247 752 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.97 % Allowed : 13.62 % Favored : 84.41 % 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: 1.31 (0.34), residues: 659 helix: 1.28 (0.27), residues: 385 sheet: -1.77 (0.69), residues: 39 loop : 0.92 (0.45), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 301 TYR 0.016 0.002 TYR A 87 PHE 0.015 0.001 PHE A 316 TRP 0.009 0.001 TRP A 59 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 ( 5525) covalent geometry : angle 0.49540 / 0.27 ( 7526) SS BOND : bond 0.00269 / 0.14 ( 2) SS BOND : angle 0.93290 / 0.53 ( 4) hydrogen bonds : bond 0.04187 / 2.63 ( 334) hydrogen bonds : angle 5.05624 / 3.67 ( 951) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 204 is missing expected H atoms. Skipping. Evaluate side-chains 94 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 80 TRP cc_start: 0.8401 (OUTLIER) cc_final: 0.7674 (t60) REVERT: A 121 ARG cc_start: 0.8330 (mtm180) cc_final: 0.7251 (mtp180) REVERT: A 304 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7655 (mm-30) REVERT: A 341 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.7103 (ptm-80) REVERT: A 359 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.7885 (m-80) REVERT: B 56 ARG cc_start: 0.8444 (tmm-80) cc_final: 0.8104 (ttp80) REVERT: B 115 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.7120 (tm-30) outliers start: 11 outliers final: 5 residues processed: 88 average time/residue: 0.9673 time to fit residues: 90.0614 Evaluate side-chains 89 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TRP Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 115 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 31 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3540 r_free = 0.3540 target = 0.138839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.124064 restraints weight = 13967.983| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 0.94 r_work: 0.3128 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 2.04 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5527 Z= 0.157 Angle : 0.493 5.237 7530 Z= 0.267 Chirality : 0.037 0.126 826 Planarity : 0.004 0.046 922 Dihedral : 6.342 67.190 752 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.61 % Allowed : 13.98 % Favored : 84.41 % 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: 1.34 (0.34), residues: 659 helix: 1.30 (0.27), residues: 385 sheet: -1.75 (0.69), residues: 39 loop : 0.93 (0.45), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 301 TYR 0.015 0.001 TYR A 87 PHE 0.015 0.001 PHE A 316 TRP 0.009 0.001 TRP A 59 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 ( 5525) covalent geometry : angle 0.49270 / 0.27 ( 7526) SS BOND : bond 0.00257 / 0.13 ( 2) SS BOND : angle 0.94799 / 0.54 ( 4) hydrogen bonds : bond 0.04185 / 2.63 ( 334) hydrogen bonds : angle 5.02858 / 3.66 ( 951) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 204 is missing expected H atoms. Skipping. Evaluate side-chains 92 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 80 TRP cc_start: 0.8398 (OUTLIER) cc_final: 0.7678 (t60) REVERT: A 121 ARG cc_start: 0.8299 (mtm180) cc_final: 0.7300 (mtp180) REVERT: A 268 THR cc_start: 0.8425 (m) cc_final: 0.8099 (p) REVERT: A 304 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7645 (mm-30) REVERT: A 359 PHE cc_start: 0.8214 (OUTLIER) cc_final: 0.7905 (m-80) REVERT: B 56 ARG cc_start: 0.8449 (tmm-80) cc_final: 0.8105 (ttp80) REVERT: B 115 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.7176 (tm-30) outliers start: 9 outliers final: 5 residues processed: 88 average time/residue: 0.9799 time to fit residues: 91.1958 Evaluate side-chains 91 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 TRP Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 115 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 73.7237 > 50: distance: 208 - 227: 33.601 distance: 227 - 228: 39.218 distance: 227 - 236: 57.226 distance: 228 - 229: 57.350 distance: 228 - 231: 69.557 distance: 228 - 237: 56.765 distance: 229 - 230: 39.386 distance: 229 - 249: 68.723 distance: 231 - 232: 38.903 distance: 231 - 238: 40.523 distance: 231 - 239: 40.427 distance: 232 - 233: 41.170 distance: 233 - 242: 40.746 distance: 234 - 244: 40.487 distance: 234 - 245: 56.388 distance: 235 - 246: 39.692 distance: 249 - 250: 69.930 distance: 249 - 260: 39.576 distance: 250 - 251: 56.342 distance: 250 - 253: 40.267 distance: 250 - 261: 40.597 distance: 251 - 252: 68.987 distance: 253 - 254: 57.176 distance: 253 - 262: 40.302 distance: 253 - 263: 56.104 distance: 254 - 255: 38.976 distance: 255 - 257: 41.097 distance: 255 - 264: 40.045 distance: 259 - 268: 56.277 distance: 269 - 276: 40.372 distance: 270 - 273: 40.542 distance: 270 - 277: 39.494 distance: 272 - 317: 39.463 distance: 273 - 274: 39.257 distance: 273 - 275: 40.772 distance: 273 - 278: 39.732 distance: 274 - 279: 56.712 distance: 283 - 284: 40.136 distance: 284 - 285: 39.674 distance: 284 - 287: 57.899 distance: 284 - 290: 56.424 distance: 285 - 297: 40.306 distance: 286 - 332: 57.283 distance: 287 - 291: 39.361 distance: 287 - 292: 39.205 distance: 288 - 289: 40.874 distance: 288 - 293: 39.848 distance: 288 - 294: 39.443 distance: 289 - 295: 39.797 distance: 289 - 296: 56.444 distance: 297 - 298: 38.818 distance: 298 - 301: 40.197 distance: 298 - 303: 56.572 distance: 299 - 307: 39.457 distance: 300 - 352: 42.736 distance: 301 - 304: 39.591 distance: 307 - 308: 57.863 distance: 307 - 312: 56.324 distance: 308 - 309: 56.536 distance: 308 - 311: 38.729 distance: 308 - 313: 38.956 distance: 310 - 373: 57.492 distance: 311 - 314: 39.878 distance: 311 - 315: 56.935 distance: 311 - 316: 56.376 distance: 317 - 318: 39.969 distance: 317 - 326: 39.806 distance: 318 - 319: 39.423 distance: 318 - 321: 57.273 distance: 318 - 327: 40.328 distance: 319 - 332: 40.831 distance: 320 - 388: 35.424 distance: 321 - 322: 68.638 distance: 321 - 328: 40.453 distance: 322 - 323: 40.843 distance: 322 - 330: 57.375 distance: 322 - 331: 40.343 distance: 323 - 324: 56.171 distance: 323 - 325: 40.308 distance: 332 - 333: 38.551 distance: 332 - 343: 39.524 distance: 333 - 334: 40.869 distance: 333 - 336: 68.736 distance: 333 - 344: 40.776 distance: 334 - 335: 39.143 distance: 334 - 352: 41.289 distance: 335 - 406: 34.117 distance: 336 - 337: 56.033 distance: 336 - 345: 40.486 distance: 336 - 346: 39.276 distance: 337 - 339: 40.504 distance: 338 - 340: 39.735 distance: 339 - 348: 56.900 distance: 340 - 342: 57.254 distance: 340 - 349: 56.589 distance: 341 - 342: 56.607 distance: 341 - 350: 56.479 distance: 342 - 351: 40.084 distance: 352 - 353: 56.875 distance: 352 - 364: 40.177 distance: 353 - 354: 40.469 distance: 353 - 356: 39.731 distance: 353 - 365: 40.147 distance: 354 - 373: 39.724 distance: 356 - 357: 57.044 distance: 356 - 366: 56.932 distance: 356 - 367: 56.508 distance: 357 - 359: 56.081 distance: 358 - 360: 39.229 distance: 358 - 368: 40.605 distance: 359 - 361: 40.684 distance: 359 - 369: 40.413 distance: 360 - 362: 57.444 distance: 360 - 370: 69.643 distance: 361 - 371: 39.343 distance: 362 - 363: 68.919 distance: 363 - 372: 57.260 distance: 373 - 374: 55.445 distance: 373 - 382: 39.705 distance: 374 - 375: 38.998 distance: 374 - 377: 40.773 distance: 374 - 383: 69.711 distance: 375 - 376: 56.071 distance: 375 - 388: 35.030 distance: 377 - 378: 68.460 distance: 377 - 384: 39.795 distance: 377 - 385: 39.448 distance: 378 - 379: 57.562 distance: 378 - 386: 69.205 distance: 378 - 387: 57.136 distance: 379 - 380: 41.188 distance: 379 - 381: 55.983