Starting phenix.real_space_refine on Fri Aug 22 16:41:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kmj_62435/08_2025/9kmj_62435.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kmj_62435/08_2025/9kmj_62435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kmj_62435/08_2025/9kmj_62435.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kmj_62435/08_2025/9kmj_62435.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kmj_62435/08_2025/9kmj_62435.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kmj_62435/08_2025/9kmj_62435.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.024 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: 6 Type Number sf(0) Gaussians S 43 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 3953 2.51 5 N 950 2.21 5 O 1070 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6019 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4282 Classifications: {'peptide': 536} Link IDs: {'PTRANS': 27, 'TRANS': 508} Chain breaks: 1 Chain: "H" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 922 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "L" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 804 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 11 Unusual residues: {' CL': 1, ' NA': 2, 'TAU': 1} Classifications: {'undetermined': 4, 'water': 1} Link IDs: {None: 4} Time building chain proxies: 1.86, per 1000 atoms: 0.31 Number of scatterers: 6019 At special positions: 0 Unit cell: (77.08, 82.82, 113.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 43 16.00 Na 2 11.00 O 1070 8.00 N 950 7.00 C 3953 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 171 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " 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: 0.55 Conformation dependent library (CDL) restraints added in 255.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1386 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 7 sheets defined 55.4% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 46 through 56 removed outlier: 4.024A pdb=" N PHE A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL A 51 " --> pdb=" O LYS A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 removed outlier: 3.614A pdb=" N VAL A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.699A pdb=" N TYR A 69 " --> pdb=" O TRP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 90 Processing helix chain 'A' and resid 90 through 106 Processing helix chain 'A' and resid 110 through 116 removed outlier: 3.605A pdb=" N LYS A 115 " --> pdb=" O CYS A 112 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE A 116 " --> pdb=" O TRP A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 120 Processing helix chain 'A' and resid 121 through 151 removed outlier: 3.733A pdb=" N TYR A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 217 through 234 Processing helix chain 'A' and resid 247 through 267 Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 269 through 279 removed outlier: 3.586A pdb=" N GLY A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 286 removed outlier: 3.558A pdb=" N LEU A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU A 286 " --> pdb=" O ILE A 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 281 through 286' Processing helix chain 'A' and resid 287 through 302 removed outlier: 4.362A pdb=" N TRP A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 315 removed outlier: 3.572A pdb=" N TYR A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 356 removed outlier: 4.593A pdb=" N ASP A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 removed outlier: 3.619A pdb=" N VAL A 362 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 379 Processing helix chain 'A' and resid 383 through 418 removed outlier: 3.906A pdb=" N TYR A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 444 Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 450 through 462 removed outlier: 3.804A pdb=" N VAL A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 482 Processing helix chain 'A' and resid 484 through 496 Processing helix chain 'A' and resid 501 through 510 removed outlier: 3.529A pdb=" N TYR A 506 " --> pdb=" O PRO A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 526 Processing helix chain 'A' and resid 539 through 555 Processing helix chain 'A' and resid 555 through 568 Processing helix chain 'A' and resid 571 through 580 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.734A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.617A pdb=" N ASP H 90 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.928A pdb=" N ALA L 84 " --> pdb=" O ALA L 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532 removed outlier: 3.552A pdb=" N TYR A 532 " --> pdb=" O TYR A 536 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.756A pdb=" N LEU H 18 " --> pdb=" O MET H 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.756A pdb=" N LEU H 18 " --> pdb=" O MET H 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.125A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 6 removed outlier: 5.927A pdb=" N THR L 70 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 10.623A pdb=" N SER L 27 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 9.999A pdb=" N SER L 68 " --> pdb=" O SER L 27 " (cutoff:3.500A) removed outlier: 11.429A pdb=" N VAL L 29 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 12.104A pdb=" N SER L 66 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.895A pdb=" N MET L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'L' and resid 54 through 55 removed outlier: 5.540A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN L 91 " --> pdb=" O THR L 98 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) 338 hydrogen bonds defined for protein. 963 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: 1.02 Time building geometry restraints manager: 0.74 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: 1761 1.34 - 1.46: 1514 1.46 - 1.58: 2855 1.58 - 1.70: 0 1.70 - 1.82: 63 Bond restraints: 6193 Sorted by residual: bond pdb=" CB PRO A 68 " pdb=" CG PRO A 68 " ideal model delta sigma weight residual 1.492 1.410 0.082 5.00e-02 4.00e+02 2.68e+00 bond pdb=" CD GLU A 406 " pdb=" OE1 GLU A 406 " ideal model delta sigma weight residual 1.249 1.220 0.029 1.90e-02 2.77e+03 2.32e+00 bond pdb=" C TYR L 95 " pdb=" N PRO L 96 " ideal model delta sigma weight residual 1.334 1.368 -0.035 2.34e-02 1.83e+03 2.18e+00 bond pdb=" CB CYS A 476 " pdb=" SG CYS A 476 " ideal model delta sigma weight residual 1.808 1.760 0.048 3.30e-02 9.18e+02 2.13e+00 bond pdb=" CB ILE A 141 " pdb=" CG1 ILE A 141 " ideal model delta sigma weight residual 1.530 1.501 0.029 2.00e-02 2.50e+03 2.04e+00 ... (remaining 6188 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 8112 2.02 - 4.04: 257 4.04 - 6.06: 33 6.06 - 8.08: 11 8.08 - 10.10: 9 Bond angle restraints: 8422 Sorted by residual: angle pdb=" C SER L 51 " pdb=" N THR L 52 " pdb=" CA THR L 52 " ideal model delta sigma weight residual 121.54 131.64 -10.10 1.91e+00 2.74e-01 2.80e+01 angle pdb=" CA PRO A 208 " pdb=" N PRO A 208 " pdb=" CD PRO A 208 " ideal model delta sigma weight residual 112.00 106.14 5.86 1.40e+00 5.10e-01 1.75e+01 angle pdb=" C GLY A 425 " pdb=" N TYR A 426 " pdb=" CA TYR A 426 " ideal model delta sigma weight residual 121.54 128.59 -7.05 1.91e+00 2.74e-01 1.36e+01 angle pdb=" C PRO A 68 " pdb=" N TYR A 69 " pdb=" CA TYR A 69 " ideal model delta sigma weight residual 121.14 114.89 6.25 1.75e+00 3.27e-01 1.27e+01 angle pdb=" C VAL A 136 " pdb=" N TYR A 137 " pdb=" CA TYR A 137 " ideal model delta sigma weight residual 121.14 114.90 6.24 1.75e+00 3.27e-01 1.27e+01 ... (remaining 8417 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 3173 16.96 - 33.92: 306 33.92 - 50.88: 60 50.88 - 67.84: 4 67.84 - 84.79: 5 Dihedral angle restraints: 3548 sinusoidal: 1358 harmonic: 2190 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 49.65 43.35 1 1.00e+01 1.00e-02 2.62e+01 dihedral pdb=" CA TYR L 95 " pdb=" C TYR L 95 " pdb=" N PRO L 96 " pdb=" CA PRO L 96 " ideal model delta harmonic sigma weight residual 180.00 156.62 23.38 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA SER A 301 " pdb=" C SER A 301 " pdb=" N TYR A 302 " pdb=" CA TYR A 302 " ideal model delta harmonic sigma weight residual 180.00 159.99 20.01 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 3545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 654 0.048 - 0.096: 196 0.096 - 0.143: 52 0.143 - 0.191: 14 0.191 - 0.239: 4 Chirality restraints: 920 Sorted by residual: chirality pdb=" CA GLU A 406 " pdb=" N GLU A 406 " pdb=" C GLU A 406 " pdb=" CB GLU A 406 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB VAL A 357 " pdb=" CA VAL A 357 " pdb=" CG1 VAL A 357 " pdb=" CG2 VAL A 357 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CG LEU A 261 " pdb=" CB LEU A 261 " pdb=" CD1 LEU A 261 " pdb=" CD2 LEU A 261 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 917 not shown) Planarity restraints: 1036 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 207 " -0.045 5.00e-02 4.00e+02 6.51e-02 6.78e+00 pdb=" N PRO A 208 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 208 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 208 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 402 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.72e+00 pdb=" C SER A 402 " 0.045 2.00e-02 2.50e+03 pdb=" O SER A 402 " -0.017 2.00e-02 2.50e+03 pdb=" N GLN A 403 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 252 " 0.042 5.00e-02 4.00e+02 6.37e-02 6.49e+00 pdb=" N PRO A 253 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 253 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 253 " 0.036 5.00e-02 4.00e+02 ... (remaining 1033 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1422 2.78 - 3.31: 5637 3.31 - 3.84: 10901 3.84 - 4.37: 12917 4.37 - 4.90: 22504 Nonbonded interactions: 53381 Sorted by model distance: nonbonded pdb=" OD1 ASP A 494 " pdb=" OH TYR H 59 " model vdw 2.251 3.040 nonbonded pdb=" NE ARG A 493 " pdb=" O GLU H 100 " model vdw 2.332 3.120 nonbonded pdb=" O ALA A 343 " pdb=" OG SER A 346 " model vdw 2.334 3.040 nonbonded pdb=" ND2 ASN A 63 " pdb=" OG SER A 337 " model vdw 2.357 3.120 nonbonded pdb=" O ASN L 2 " pdb=" OG1 THR L 98 " model vdw 2.362 3.040 ... (remaining 53376 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: 5.050 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: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.210 Find NCS groups from input model: 0.020 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 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 : 0.006 0.082 6196 Z= 0.253 Angle : 0.877 10.105 8428 Z= 0.465 Chirality : 0.052 0.239 920 Planarity : 0.007 0.065 1036 Dihedral : 13.752 84.794 2153 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.43 (0.29), residues: 754 helix: -0.67 (0.24), residues: 364 sheet: -1.15 (0.52), residues: 103 loop : -0.99 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 62 TYR 0.026 0.002 TYR A 137 PHE 0.042 0.003 PHE A 338 TRP 0.031 0.002 TRP A 44 HIS 0.003 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00619 ( 6193) covalent geometry : angle 0.87585 ( 8422) SS BOND : bond 0.00372 ( 3) SS BOND : angle 1.60857 ( 6) hydrogen bonds : bond 0.16404 ( 329) hydrogen bonds : angle 7.43160 ( 963) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.159 Fit side-chains REVERT: H 32 TYR cc_start: 0.7454 (m-80) cc_final: 0.7181 (m-80) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.0790 time to fit residues: 10.9450 Evaluate side-chains 93 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.0270 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.169949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.135482 restraints weight = 6583.472| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.97 r_work: 0.3342 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6196 Z= 0.173 Angle : 0.614 7.745 8428 Z= 0.321 Chirality : 0.042 0.153 920 Planarity : 0.005 0.052 1036 Dihedral : 5.384 57.790 835 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.15 % Allowed : 5.08 % Favored : 94.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.30), residues: 754 helix: 0.36 (0.26), residues: 366 sheet: -0.84 (0.52), residues: 98 loop : -0.78 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 66 TYR 0.021 0.001 TYR A 137 PHE 0.022 0.002 PHE A 338 TRP 0.019 0.002 TRP A 470 HIS 0.004 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 6193) covalent geometry : angle 0.61330 ( 8422) SS BOND : bond 0.00229 ( 3) SS BOND : angle 0.97574 ( 6) hydrogen bonds : bond 0.04973 ( 329) hydrogen bonds : angle 5.48840 ( 963) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.237 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 104 average time/residue: 0.0793 time to fit residues: 11.2401 Evaluate side-chains 98 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 50 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 59 optimal weight: 0.2980 chunk 25 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 4 optimal weight: 0.0870 chunk 52 optimal weight: 0.3980 chunk 67 optimal weight: 0.9980 chunk 37 optimal weight: 0.0670 overall best weight: 0.2896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.176332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.144664 restraints weight = 6453.825| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.01 r_work: 0.3481 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6196 Z= 0.129 Angle : 0.550 7.616 8428 Z= 0.286 Chirality : 0.040 0.150 920 Planarity : 0.005 0.048 1036 Dihedral : 5.104 59.101 835 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.62 % Allowed : 9.09 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.31), residues: 754 helix: 0.98 (0.27), residues: 362 sheet: -0.53 (0.52), residues: 98 loop : -0.73 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 66 TYR 0.021 0.001 TYR A 137 PHE 0.019 0.002 PHE A 350 TRP 0.016 0.001 TRP A 470 HIS 0.002 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 6193) covalent geometry : angle 0.54945 ( 8422) SS BOND : bond 0.00215 ( 3) SS BOND : angle 0.77687 ( 6) hydrogen bonds : bond 0.04357 ( 329) hydrogen bonds : angle 5.01074 ( 963) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 0.182 Fit side-chains REVERT: H 56 ARG cc_start: 0.8506 (mtp-110) cc_final: 0.7914 (mtp180) outliers start: 4 outliers final: 2 residues processed: 99 average time/residue: 0.0878 time to fit residues: 11.5195 Evaluate side-chains 96 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 94 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 496 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 52 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 3 optimal weight: 0.0980 chunk 47 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.172762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.137850 restraints weight = 6536.258| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.00 r_work: 0.3387 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6196 Z= 0.172 Angle : 0.568 7.601 8428 Z= 0.296 Chirality : 0.041 0.154 920 Planarity : 0.005 0.070 1036 Dihedral : 5.091 59.727 835 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.08 % Allowed : 11.09 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.31), residues: 754 helix: 1.16 (0.28), residues: 362 sheet: -0.35 (0.52), residues: 97 loop : -0.65 (0.38), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 66 TYR 0.022 0.001 TYR A 137 PHE 0.021 0.002 PHE A 404 TRP 0.016 0.001 TRP A 470 HIS 0.003 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 6193) covalent geometry : angle 0.56805 ( 8422) SS BOND : bond 0.00260 ( 3) SS BOND : angle 0.67732 ( 6) hydrogen bonds : bond 0.04569 ( 329) hydrogen bonds : angle 4.97182 ( 963) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.173 Fit side-chains REVERT: A 395 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.7733 (mp) outliers start: 7 outliers final: 3 residues processed: 97 average time/residue: 0.0879 time to fit residues: 11.2183 Evaluate side-chains 95 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 91 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain L residue 21 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 41 optimal weight: 0.8980 chunk 29 optimal weight: 0.0980 chunk 26 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 19 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.172549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.139929 restraints weight = 6601.474| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.01 r_work: 0.3383 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6196 Z= 0.162 Angle : 0.557 7.704 8428 Z= 0.290 Chirality : 0.040 0.152 920 Planarity : 0.005 0.066 1036 Dihedral : 5.019 58.944 835 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.08 % Allowed : 12.94 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.31), residues: 754 helix: 1.25 (0.28), residues: 362 sheet: -0.54 (0.51), residues: 103 loop : -0.51 (0.39), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 66 TYR 0.022 0.001 TYR A 137 PHE 0.025 0.002 PHE A 404 TRP 0.017 0.001 TRP A 470 HIS 0.002 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 6193) covalent geometry : angle 0.55739 ( 8422) SS BOND : bond 0.00247 ( 3) SS BOND : angle 0.59576 ( 6) hydrogen bonds : bond 0.04475 ( 329) hydrogen bonds : angle 4.90866 ( 963) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.156 Fit side-chains REVERT: A 69 TYR cc_start: 0.8715 (OUTLIER) cc_final: 0.6601 (p90) REVERT: A 395 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.7730 (mp) outliers start: 7 outliers final: 5 residues processed: 95 average time/residue: 0.0744 time to fit residues: 9.4065 Evaluate side-chains 97 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain L residue 21 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 61 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 47 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.166695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.131970 restraints weight = 6638.799| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.97 r_work: 0.3361 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 6196 Z= 0.199 Angle : 0.585 7.828 8428 Z= 0.304 Chirality : 0.041 0.155 920 Planarity : 0.005 0.062 1036 Dihedral : 5.105 59.838 835 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.23 % Allowed : 12.94 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.32), residues: 754 helix: 1.23 (0.28), residues: 362 sheet: -0.48 (0.53), residues: 98 loop : -0.51 (0.38), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 66 TYR 0.023 0.001 TYR A 137 PHE 0.029 0.002 PHE A 404 TRP 0.017 0.001 TRP A 470 HIS 0.004 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 6193) covalent geometry : angle 0.58530 ( 8422) SS BOND : bond 0.00287 ( 3) SS BOND : angle 0.63412 ( 6) hydrogen bonds : bond 0.04709 ( 329) hydrogen bonds : angle 4.99446 ( 963) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.215 Fit side-chains REVERT: A 69 TYR cc_start: 0.8809 (OUTLIER) cc_final: 0.6665 (p90) REVERT: A 395 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.7669 (mp) REVERT: L 91 GLN cc_start: 0.9110 (pp30) cc_final: 0.8321 (pp30) outliers start: 8 outliers final: 5 residues processed: 102 average time/residue: 0.0778 time to fit residues: 10.5582 Evaluate side-chains 101 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain L residue 21 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 20 optimal weight: 0.6980 chunk 57 optimal weight: 0.0870 chunk 3 optimal weight: 0.1980 chunk 49 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 48 optimal weight: 0.0470 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.173969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.139305 restraints weight = 6551.131| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.00 r_work: 0.3377 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6196 Z= 0.133 Angle : 0.546 7.825 8428 Z= 0.282 Chirality : 0.040 0.150 920 Planarity : 0.005 0.054 1036 Dihedral : 4.936 59.627 835 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.54 % Allowed : 13.10 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.32), residues: 754 helix: 1.37 (0.27), residues: 362 sheet: -0.23 (0.51), residues: 104 loop : -0.34 (0.39), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 66 TYR 0.021 0.001 TYR A 137 PHE 0.030 0.002 PHE A 404 TRP 0.017 0.001 TRP A 470 HIS 0.002 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 6193) covalent geometry : angle 0.54560 ( 8422) SS BOND : bond 0.00232 ( 3) SS BOND : angle 0.52651 ( 6) hydrogen bonds : bond 0.04284 ( 329) hydrogen bonds : angle 4.81757 ( 963) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.168 Fit side-chains REVERT: A 69 TYR cc_start: 0.8671 (OUTLIER) cc_final: 0.6307 (p90) REVERT: A 395 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.7648 (mp) REVERT: L 17 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7807 (tm-30) REVERT: L 91 GLN cc_start: 0.9074 (pp30) cc_final: 0.8286 (pp30) outliers start: 10 outliers final: 6 residues processed: 98 average time/residue: 0.0687 time to fit residues: 9.1039 Evaluate side-chains 97 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain L residue 21 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.4863 > 50: distance: 28 - 39: 4.451 distance: 39 - 40: 9.997 distance: 40 - 41: 6.239 distance: 40 - 43: 5.595 distance: 41 - 42: 16.893 distance: 41 - 48: 24.971 distance: 43 - 44: 6.979 distance: 45 - 46: 3.006 distance: 48 - 49: 22.449 distance: 49 - 50: 33.528 distance: 50 - 51: 34.432 distance: 50 - 52: 16.896 distance: 52 - 53: 22.344 distance: 53 - 54: 30.193 distance: 53 - 56: 18.069 distance: 54 - 55: 6.648 distance: 54 - 59: 36.898 distance: 56 - 57: 34.930 distance: 56 - 58: 36.515 distance: 59 - 60: 8.414 distance: 60 - 61: 23.399 distance: 60 - 63: 23.609 distance: 61 - 62: 24.602 distance: 61 - 70: 15.535 distance: 63 - 64: 17.480 distance: 64 - 65: 7.801 distance: 65 - 66: 14.896 distance: 66 - 67: 5.618 distance: 67 - 68: 3.947 distance: 67 - 69: 6.776 distance: 70 - 71: 27.191 distance: 71 - 72: 10.535 distance: 71 - 74: 34.162 distance: 72 - 73: 5.002 distance: 72 - 76: 40.508 distance: 74 - 75: 19.653 distance: 76 - 77: 20.899 distance: 77 - 78: 29.148 distance: 77 - 80: 17.918 distance: 78 - 79: 28.615 distance: 78 - 83: 16.934 distance: 80 - 81: 31.168 distance: 80 - 82: 24.135 distance: 83 - 84: 16.248 distance: 84 - 85: 24.695 distance: 85 - 86: 8.308 distance: 85 - 87: 31.221 distance: 87 - 88: 18.999 distance: 88 - 89: 14.985 distance: 88 - 91: 5.473 distance: 89 - 90: 26.408 distance: 89 - 96: 18.916 distance: 91 - 92: 3.920 distance: 92 - 93: 13.144 distance: 93 - 94: 11.916 distance: 94 - 95: 9.445 distance: 96 - 97: 13.665 distance: 97 - 98: 30.580 distance: 97 - 100: 37.041 distance: 98 - 99: 19.343 distance: 98 - 103: 27.656 distance: 100 - 101: 41.537 distance: 100 - 102: 21.757 distance: 103 - 104: 11.920 distance: 104 - 105: 4.830 distance: 104 - 107: 12.464 distance: 105 - 106: 17.464 distance: 105 - 110: 4.100 distance: 107 - 108: 10.971 distance: 107 - 109: 18.189