Starting phenix.real_space_refine on Sat May 2 15:32:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v93_64859/05_2026/9v93_64859.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v93_64859/05_2026/9v93_64859.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9v93_64859/05_2026/9v93_64859.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v93_64859/05_2026/9v93_64859.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9v93_64859/05_2026/9v93_64859.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v93_64859/05_2026/9v93_64859.map" } resolution = 2.81 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= 0.039 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 P 32 5.49 5 Mg 3 5.21 5 S 15 5.16 5 C 4128 2.51 5 N 1221 2.21 5 O 1325 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6724 Number of models: 1 Model: "" Number of chains: 4 Chain: "a" Number of atoms: 6050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 6050 Classifications: {'peptide': 760} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 42, 'TRANS': 717} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "b" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 359 Classifications: {'DNA': 17} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 16} Chain: "c" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 310 Classifications: {'RNA': 15} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 9} Link IDs: {'rna3p': 14} Chain: "a" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3, 'water': 2} Link IDs: {None: 4} Time building chain proxies: 1.85, per 1000 atoms: 0.28 Number of scatterers: 6724 At special positions: 0 Unit cell: (89.355, 86.802, 102.971, 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) S 15 16.00 P 32 15.00 Mg 3 11.99 O 1325 8.00 N 1221 7.00 C 4128 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 367.1 milliseconds 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1412 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 8 sheets defined 34.1% alpha, 23.2% beta 11 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'a' and resid 37 through 54 removed outlier: 3.585A pdb=" N GLN a 48 " --> pdb=" O ARG a 44 " (cutoff:3.500A) Processing helix chain 'a' and resid 109 through 130 removed outlier: 3.654A pdb=" N ALA a 127 " --> pdb=" O ALA a 123 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE a 128 " --> pdb=" O ILE a 124 " (cutoff:3.500A) Processing helix chain 'a' and resid 195 through 203 Processing helix chain 'a' and resid 203 through 208 Processing helix chain 'a' and resid 212 through 216 removed outlier: 3.948A pdb=" N ARG a 216 " --> pdb=" O ALA a 213 " (cutoff:3.500A) Processing helix chain 'a' and resid 254 through 263 Processing helix chain 'a' and resid 299 through 304 Processing helix chain 'a' and resid 312 through 324 Processing helix chain 'a' and resid 325 through 327 No H-bonds generated for 'chain 'a' and resid 325 through 327' Processing helix chain 'a' and resid 360 through 362 No H-bonds generated for 'chain 'a' and resid 360 through 362' Processing helix chain 'a' and resid 372 through 392 removed outlier: 4.492A pdb=" N MET a 385 " --> pdb=" O ARG a 381 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR a 386 " --> pdb=" O GLN a 382 " (cutoff:3.500A) Processing helix chain 'a' and resid 411 through 431 Processing helix chain 'a' and resid 451 through 464 Processing helix chain 'a' and resid 481 through 491 removed outlier: 4.514A pdb=" N ASP a 485 " --> pdb=" O GLU a 481 " (cutoff:3.500A) Processing helix chain 'a' and resid 501 through 510 Processing helix chain 'a' and resid 516 through 531 Processing helix chain 'a' and resid 587 through 606 Processing helix chain 'a' and resid 621 through 638 Processing helix chain 'a' and resid 697 through 702 Processing helix chain 'a' and resid 723 through 734 Processing helix chain 'a' and resid 749 through 763 removed outlier: 4.263A pdb=" N SER a 755 " --> pdb=" O THR a 751 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU a 761 " --> pdb=" O GLU a 757 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE a 762 " --> pdb=" O ARG a 758 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 344 through 346 removed outlier: 3.553A pdb=" N PHE a 344 " --> pdb=" O ALA a 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 135 through 139 removed outlier: 5.686A pdb=" N ARG a 137 " --> pdb=" O PHE a 144 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N PHE a 144 " --> pdb=" O ARG a 137 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ARG a 162 " --> pdb=" O ARG a 145 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL a 330 " --> pdb=" O LEU a 337 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 58 through 60 removed outlier: 3.687A pdb=" N ALA a 67 " --> pdb=" O THR a 60 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR a 70 " --> pdb=" O ARG a 24 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL a 25 " --> pdb=" O ILE a 97 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE a 97 " --> pdb=" O VAL a 25 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG a 90 " --> pdb=" O ASP a 86 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 286 through 287 removed outlier: 7.563A pdb=" N ALA a 272 " --> pdb=" O THR a 236 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY a 234 " --> pdb=" O PHE a 274 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ARG a 276 " --> pdb=" O PHE a 232 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N PHE a 232 " --> pdb=" O ARG a 276 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 244 through 247 Processing sheet with id=AA6, first strand: chain 'a' and resid 364 through 365 Processing sheet with id=AA7, first strand: chain 'a' and resid 436 through 442 removed outlier: 6.785A pdb=" N LEU a 402 " --> pdb=" O ARG a 438 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N ILE a 440 " --> pdb=" O LEU a 402 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LEU a 404 " --> pdb=" O ILE a 440 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N TYR a 442 " --> pdb=" O LEU a 404 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N TYR a 406 " --> pdb=" O TYR a 442 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ASP a 401 " --> pdb=" O LEU a 470 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL a 472 " --> pdb=" O ASP a 401 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N VAL a 403 " --> pdb=" O VAL a 472 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL a 474 " --> pdb=" O VAL a 403 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU a 405 " --> pdb=" O VAL a 474 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N GLN a 497 " --> pdb=" O PHE a 469 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL a 499 " --> pdb=" O PRO a 471 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE a 473 " --> pdb=" O VAL a 499 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'a' and resid 568 through 575 removed outlier: 6.301A pdb=" N LEU a 551 " --> pdb=" O ASP a 617 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU a 612 " --> pdb=" O GLY a 648 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL a 650 " --> pdb=" O LEU a 612 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N VAL a 614 " --> pdb=" O VAL a 650 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL a 652 " --> pdb=" O VAL a 614 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ARG a 616 " --> pdb=" O VAL a 652 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL a 649 " --> pdb=" O THR a 714 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER a 679 " --> pdb=" O THR a 691 " (cutoff:3.500A) 269 hydrogen bonds defined for protein. 759 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 27 hydrogen bonds 54 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 1.21 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1799 1.33 - 1.45: 1362 1.45 - 1.57: 3683 1.57 - 1.69: 62 1.69 - 1.81: 23 Bond restraints: 6929 Sorted by residual: bond pdb=" C THR a 244 " pdb=" N PHE a 245 " ideal model delta sigma weight residual 1.331 1.308 0.023 1.59e-02 3.96e+03 2.08e+00 bond pdb=" N PRO a 88 " pdb=" CA PRO a 88 " ideal model delta sigma weight residual 1.469 1.477 -0.008 7.40e-03 1.83e+04 1.25e+00 bond pdb=" N ALA a 18 " pdb=" CA ALA a 18 " ideal model delta sigma weight residual 1.457 1.472 -0.014 1.29e-02 6.01e+03 1.21e+00 bond pdb=" C3' DT b 13 " pdb=" O3' DT b 13 " ideal model delta sigma weight residual 1.422 1.453 -0.031 3.00e-02 1.11e+03 1.07e+00 bond pdb=" CA GLY a 548 " pdb=" C GLY a 548 " ideal model delta sigma weight residual 1.517 1.512 0.006 7.00e-03 2.04e+04 7.02e-01 ... (remaining 6924 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 9136 1.22 - 2.43: 342 2.43 - 3.65: 56 3.65 - 4.86: 9 4.86 - 6.08: 6 Bond angle restraints: 9549 Sorted by residual: angle pdb=" N ILE a 752 " pdb=" CA ILE a 752 " pdb=" C ILE a 752 " ideal model delta sigma weight residual 111.90 109.57 2.33 8.10e-01 1.52e+00 8.26e+00 angle pdb=" C ALA a 18 " pdb=" CA ALA a 18 " pdb=" CB ALA a 18 " ideal model delta sigma weight residual 110.42 115.78 -5.36 1.99e+00 2.53e-01 7.25e+00 angle pdb=" C GLN a 19 " pdb=" CA GLN a 19 " pdb=" CB GLN a 19 " ideal model delta sigma weight residual 110.42 115.49 -5.07 1.99e+00 2.53e-01 6.49e+00 angle pdb=" C ASP a 222 " pdb=" N ASN a 223 " pdb=" CA ASN a 223 " ideal model delta sigma weight residual 120.89 117.77 3.12 1.50e+00 4.44e-01 4.32e+00 angle pdb=" N VAL a 207 " pdb=" CA VAL a 207 " pdb=" C VAL a 207 " ideal model delta sigma weight residual 109.34 113.28 -3.94 2.08e+00 2.31e-01 3.58e+00 ... (remaining 9544 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.30: 3894 27.30 - 54.60: 203 54.60 - 81.90: 34 81.90 - 109.20: 3 109.20 - 136.50: 1 Dihedral angle restraints: 4135 sinusoidal: 1943 harmonic: 2192 Sorted by residual: dihedral pdb=" CA ASN a 223 " pdb=" C ASN a 223 " pdb=" N GLY a 224 " pdb=" CA GLY a 224 " ideal model delta harmonic sigma weight residual 180.00 155.95 24.05 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" C4' DT b 13 " pdb=" C3' DT b 13 " pdb=" O3' DT b 13 " pdb=" P DT b 14 " ideal model delta sinusoidal sigma weight residual 220.00 83.50 136.50 1 3.50e+01 8.16e-04 1.35e+01 dihedral pdb=" CA PRO a 372 " pdb=" C PRO a 372 " pdb=" N ILE a 373 " pdb=" CA ILE a 373 " ideal model delta harmonic sigma weight residual -180.00 -161.69 -18.31 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 4132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 633 0.028 - 0.057: 283 0.057 - 0.085: 88 0.085 - 0.113: 45 0.113 - 0.141: 19 Chirality restraints: 1068 Sorted by residual: chirality pdb=" CA ILE a 94 " pdb=" N ILE a 94 " pdb=" C ILE a 94 " pdb=" CB ILE a 94 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA VAL a 561 " pdb=" N VAL a 561 " pdb=" C VAL a 561 " pdb=" CB VAL a 561 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA ILE a 689 " pdb=" N ILE a 689 " pdb=" C ILE a 689 " pdb=" CB ILE a 689 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 ... (remaining 1065 not shown) Planarity restraints: 1138 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS a 174 " -0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO a 175 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO a 175 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO a 175 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL a 266 " 0.027 5.00e-02 4.00e+02 4.05e-02 2.62e+00 pdb=" N PRO a 267 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO a 267 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO a 267 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN a 716 " -0.024 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO a 717 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO a 717 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO a 717 " -0.021 5.00e-02 4.00e+02 ... (remaining 1135 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 574 2.74 - 3.28: 5973 3.28 - 3.82: 10861 3.82 - 4.36: 13755 4.36 - 4.90: 22764 Nonbonded interactions: 53927 Sorted by model distance: nonbonded pdb=" OP1 U c 7 " pdb="MG MG a 802 " model vdw 2.201 2.170 nonbonded pdb=" NE2 GLN a 85 " pdb=" O ARG a 90 " model vdw 2.257 3.120 nonbonded pdb=" NZ LYS a 654 " pdb=" OP2 U c 7 " model vdw 2.276 3.120 nonbonded pdb=" OE1 GLU a 651 " pdb=" OG1 THR a 714 " model vdw 2.295 3.040 nonbonded pdb=" NZ LYS a 596 " pdb=" OE1 GLU a 634 " model vdw 2.335 3.120 ... (remaining 53922 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: 1.970 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: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.010 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6929 Z= 0.160 Angle : 0.567 6.081 9549 Z= 0.318 Chirality : 0.041 0.141 1068 Planarity : 0.005 0.044 1138 Dihedral : 15.762 136.504 2723 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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: 0.66 (0.30), residues: 758 helix: 1.47 (0.34), residues: 231 sheet: 0.56 (0.39), residues: 181 loop : -0.27 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG a 490 TYR 0.013 0.001 TYR a 380 PHE 0.019 0.002 PHE a 232 TRP 0.017 0.002 TRP a 65 HIS 0.006 0.001 HIS a 186 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 6929) covalent geometry : angle 0.56706 ( 9549) hydrogen bonds : bond 0.17209 ( 296) hydrogen bonds : angle 7.03880 ( 813) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.244 Fit side-chains REVERT: a 361 ASN cc_start: 0.7386 (m-40) cc_final: 0.7181 (t0) REVERT: a 646 GLN cc_start: 0.7700 (mt0) cc_final: 0.7411 (mt0) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.5922 time to fit residues: 56.0160 Evaluate side-chains 67 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.1980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 341 HIS a 482 HIS a 590 GLN a 685 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.176115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.136378 restraints weight = 7131.715| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.28 r_work: 0.3267 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6929 Z= 0.137 Angle : 0.525 6.106 9549 Z= 0.282 Chirality : 0.042 0.135 1068 Planarity : 0.005 0.045 1138 Dihedral : 14.943 140.374 1249 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.39 % Allowed : 6.80 % Favored : 91.81 % 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: 1.01 (0.30), residues: 758 helix: 1.97 (0.34), residues: 232 sheet: 0.63 (0.40), residues: 181 loop : -0.15 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG a 290 TYR 0.014 0.001 TYR a 380 PHE 0.013 0.002 PHE a 545 TRP 0.009 0.001 TRP a 136 HIS 0.004 0.001 HIS a 139 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 6929) covalent geometry : angle 0.52488 ( 9549) hydrogen bonds : bond 0.04456 ( 296) hydrogen bonds : angle 5.13061 ( 813) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.252 Fit side-chains REVERT: a 54 LYS cc_start: 0.8238 (mtpt) cc_final: 0.7252 (mptp) REVERT: a 276 ARG cc_start: 0.6217 (tpt90) cc_final: 0.5954 (tpt90) REVERT: a 361 ASN cc_start: 0.7838 (m-40) cc_final: 0.7247 (t0) REVERT: a 390 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7846 (tm-30) REVERT: a 745 GLU cc_start: 0.8210 (mp0) cc_final: 0.7792 (mp0) outliers start: 9 outliers final: 2 residues processed: 71 average time/residue: 0.6292 time to fit residues: 46.9557 Evaluate side-chains 64 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 336 THR Chi-restraints excluded: chain a residue 390 GLU Chi-restraints excluded: chain a residue 427 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 5 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 44 optimal weight: 0.0040 chunk 11 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 482 HIS a 685 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.171959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.131275 restraints weight = 7027.194| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.06 r_work: 0.3236 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6929 Z= 0.145 Angle : 0.520 5.343 9549 Z= 0.278 Chirality : 0.042 0.137 1068 Planarity : 0.005 0.046 1138 Dihedral : 14.939 141.741 1249 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.70 % Allowed : 8.81 % Favored : 89.49 % 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: 1.08 (0.30), residues: 758 helix: 2.08 (0.34), residues: 234 sheet: 0.67 (0.41), residues: 176 loop : -0.15 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG a 290 TYR 0.014 0.001 TYR a 380 PHE 0.014 0.002 PHE a 545 TRP 0.010 0.001 TRP a 136 HIS 0.004 0.001 HIS a 139 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 6929) covalent geometry : angle 0.51973 ( 9549) hydrogen bonds : bond 0.04193 ( 296) hydrogen bonds : angle 4.83816 ( 813) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: a 54 LYS cc_start: 0.8210 (mtpt) cc_final: 0.7153 (mptp) REVERT: a 99 GLU cc_start: 0.7040 (mp0) cc_final: 0.6730 (mp0) REVERT: a 276 ARG cc_start: 0.6394 (tpt90) cc_final: 0.6114 (tpt90) REVERT: a 361 ASN cc_start: 0.7940 (m-40) cc_final: 0.7243 (t0) REVERT: a 373 ILE cc_start: 0.7805 (mp) cc_final: 0.7554 (mm) REVERT: a 390 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7538 (tm-30) REVERT: a 417 LYS cc_start: 0.7519 (mppt) cc_final: 0.6998 (mtmt) REVERT: a 745 GLU cc_start: 0.8196 (mp0) cc_final: 0.7823 (mp0) outliers start: 11 outliers final: 4 residues processed: 75 average time/residue: 0.7107 time to fit residues: 55.7270 Evaluate side-chains 73 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 103 VAL Chi-restraints excluded: chain a residue 336 THR Chi-restraints excluded: chain a residue 390 GLU Chi-restraints excluded: chain a residue 427 LYS Chi-restraints excluded: chain a residue 435 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 43 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 chunk 54 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 8 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 482 HIS a 590 GLN a 685 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.172463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.131407 restraints weight = 7149.996| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.25 r_work: 0.3240 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6929 Z= 0.131 Angle : 0.496 4.992 9549 Z= 0.266 Chirality : 0.041 0.137 1068 Planarity : 0.004 0.043 1138 Dihedral : 14.863 141.027 1249 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.55 % Allowed : 9.74 % Favored : 88.72 % 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: 1.17 (0.30), residues: 758 helix: 2.18 (0.34), residues: 235 sheet: 0.74 (0.41), residues: 176 loop : -0.14 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG a 290 TYR 0.012 0.001 TYR a 380 PHE 0.013 0.001 PHE a 545 TRP 0.010 0.001 TRP a 136 HIS 0.003 0.001 HIS a 139 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 6929) covalent geometry : angle 0.49616 ( 9549) hydrogen bonds : bond 0.03820 ( 296) hydrogen bonds : angle 4.67938 ( 813) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: a 54 LYS cc_start: 0.8234 (mtpt) cc_final: 0.7218 (mptp) REVERT: a 153 ASP cc_start: 0.7629 (OUTLIER) cc_final: 0.7281 (t70) REVERT: a 276 ARG cc_start: 0.6504 (tpt90) cc_final: 0.6214 (tpt90) REVERT: a 361 ASN cc_start: 0.7892 (m-40) cc_final: 0.7203 (t0) REVERT: a 390 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7490 (tm-30) REVERT: a 417 LYS cc_start: 0.7589 (mppt) cc_final: 0.7102 (mtmt) REVERT: a 424 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7680 (tp30) REVERT: a 745 GLU cc_start: 0.8194 (mp0) cc_final: 0.7845 (mp0) REVERT: a 761 GLU cc_start: 0.6057 (mt-10) cc_final: 0.5665 (mm-30) outliers start: 10 outliers final: 4 residues processed: 80 average time/residue: 0.7107 time to fit residues: 59.3304 Evaluate side-chains 75 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 103 VAL Chi-restraints excluded: chain a residue 153 ASP Chi-restraints excluded: chain a residue 336 THR Chi-restraints excluded: chain a residue 390 GLU Chi-restraints excluded: chain a residue 427 LYS Chi-restraints excluded: chain a residue 435 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 4 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 35 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 482 HIS a 590 GLN a 685 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.172600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.133481 restraints weight = 7187.970| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.05 r_work: 0.3264 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6929 Z= 0.125 Angle : 0.489 5.002 9549 Z= 0.263 Chirality : 0.041 0.136 1068 Planarity : 0.004 0.042 1138 Dihedral : 14.833 141.078 1249 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.32 % Allowed : 9.43 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.30), residues: 758 helix: 2.26 (0.34), residues: 236 sheet: 0.85 (0.41), residues: 173 loop : -0.17 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG a 290 TYR 0.015 0.001 TYR a 406 PHE 0.012 0.001 PHE a 545 TRP 0.009 0.001 TRP a 570 HIS 0.003 0.001 HIS a 139 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 6929) covalent geometry : angle 0.48850 ( 9549) hydrogen bonds : bond 0.03673 ( 296) hydrogen bonds : angle 4.57790 ( 813) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: a 54 LYS cc_start: 0.8242 (mtpt) cc_final: 0.7237 (mptp) REVERT: a 99 GLU cc_start: 0.7056 (mt-10) cc_final: 0.6740 (mp0) REVERT: a 153 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7277 (t70) REVERT: a 276 ARG cc_start: 0.6555 (tpt90) cc_final: 0.6254 (tpt90) REVERT: a 325 ASN cc_start: 0.8805 (OUTLIER) cc_final: 0.8543 (t0) REVERT: a 361 ASN cc_start: 0.7867 (m-40) cc_final: 0.7254 (t0) REVERT: a 390 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7490 (tm-30) REVERT: a 412 ARG cc_start: 0.6863 (OUTLIER) cc_final: 0.6533 (tmm160) REVERT: a 417 LYS cc_start: 0.7611 (mppt) cc_final: 0.7350 (mtmt) REVERT: a 424 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7597 (tp30) REVERT: a 745 GLU cc_start: 0.8156 (mp0) cc_final: 0.7815 (mp0) REVERT: a 761 GLU cc_start: 0.5965 (mt-10) cc_final: 0.5600 (mm-30) outliers start: 15 outliers final: 6 residues processed: 78 average time/residue: 0.7276 time to fit residues: 59.2780 Evaluate side-chains 78 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 103 VAL Chi-restraints excluded: chain a residue 153 ASP Chi-restraints excluded: chain a residue 325 ASN Chi-restraints excluded: chain a residue 336 THR Chi-restraints excluded: chain a residue 390 GLU Chi-restraints excluded: chain a residue 412 ARG Chi-restraints excluded: chain a residue 427 LYS Chi-restraints excluded: chain a residue 435 ARG Chi-restraints excluded: chain a residue 586 ILE Chi-restraints excluded: chain a residue 684 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 13 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 482 HIS a 590 GLN a 685 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.171008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.130796 restraints weight = 7165.238| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.18 r_work: 0.3213 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6929 Z= 0.156 Angle : 0.521 5.103 9549 Z= 0.278 Chirality : 0.042 0.145 1068 Planarity : 0.005 0.044 1138 Dihedral : 14.908 142.274 1249 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.16 % Allowed : 10.36 % Favored : 87.48 % 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: 1.11 (0.30), residues: 758 helix: 2.17 (0.34), residues: 235 sheet: 0.78 (0.41), residues: 173 loop : -0.25 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG a 290 TYR 0.013 0.001 TYR a 380 PHE 0.014 0.002 PHE a 545 TRP 0.010 0.001 TRP a 136 HIS 0.004 0.001 HIS a 139 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 6929) covalent geometry : angle 0.52124 ( 9549) hydrogen bonds : bond 0.04153 ( 296) hydrogen bonds : angle 4.64424 ( 813) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: a 54 LYS cc_start: 0.8255 (mtpt) cc_final: 0.7233 (mptp) REVERT: a 153 ASP cc_start: 0.7607 (OUTLIER) cc_final: 0.7303 (t70) REVERT: a 276 ARG cc_start: 0.6605 (tpt90) cc_final: 0.6282 (tpt90) REVERT: a 361 ASN cc_start: 0.7931 (m-40) cc_final: 0.7294 (t0) REVERT: a 390 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7538 (tm-30) REVERT: a 412 ARG cc_start: 0.6908 (OUTLIER) cc_final: 0.6577 (tmm160) REVERT: a 415 ARG cc_start: 0.6946 (ttp80) cc_final: 0.6671 (ttp-170) REVERT: a 417 LYS cc_start: 0.7671 (mppt) cc_final: 0.7359 (mppt) REVERT: a 745 GLU cc_start: 0.8179 (mp0) cc_final: 0.7839 (mp0) REVERT: a 761 GLU cc_start: 0.6074 (mt-10) cc_final: 0.5681 (mm-30) outliers start: 14 outliers final: 7 residues processed: 80 average time/residue: 0.7440 time to fit residues: 61.9956 Evaluate side-chains 84 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 103 VAL Chi-restraints excluded: chain a residue 153 ASP Chi-restraints excluded: chain a residue 158 VAL Chi-restraints excluded: chain a residue 336 THR Chi-restraints excluded: chain a residue 390 GLU Chi-restraints excluded: chain a residue 412 ARG Chi-restraints excluded: chain a residue 427 LYS Chi-restraints excluded: chain a residue 435 ARG Chi-restraints excluded: chain a residue 586 ILE Chi-restraints excluded: chain a residue 684 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 39 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 5 optimal weight: 0.1980 chunk 37 optimal weight: 0.3980 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 482 HIS a 590 GLN a 685 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.174366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.134466 restraints weight = 7090.245| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.06 r_work: 0.3275 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 6929 Z= 0.104 Angle : 0.459 4.949 9549 Z= 0.248 Chirality : 0.040 0.144 1068 Planarity : 0.004 0.038 1138 Dihedral : 14.765 140.086 1249 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.16 % Allowed : 11.13 % Favored : 86.71 % 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: 1.35 (0.31), residues: 758 helix: 2.42 (0.34), residues: 236 sheet: 0.80 (0.41), residues: 176 loop : -0.09 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG a 290 TYR 0.014 0.001 TYR a 380 PHE 0.011 0.001 PHE a 545 TRP 0.011 0.001 TRP a 570 HIS 0.002 0.001 HIS a 139 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 6929) covalent geometry : angle 0.45944 ( 9549) hydrogen bonds : bond 0.03244 ( 296) hydrogen bonds : angle 4.39227 ( 813) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: a 14 THR cc_start: 0.8033 (p) cc_final: 0.7825 (p) REVERT: a 54 LYS cc_start: 0.8254 (mtpt) cc_final: 0.7254 (mptp) REVERT: a 276 ARG cc_start: 0.6604 (tpt90) cc_final: 0.6282 (tpt90) REVERT: a 328 ARG cc_start: 0.7720 (mmt180) cc_final: 0.7516 (mmt180) REVERT: a 361 ASN cc_start: 0.7855 (m-40) cc_final: 0.7285 (t0) REVERT: a 390 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7442 (tm-30) REVERT: a 412 ARG cc_start: 0.6866 (OUTLIER) cc_final: 0.6511 (tmm-80) REVERT: a 417 LYS cc_start: 0.7654 (mppt) cc_final: 0.7361 (mtmt) REVERT: a 424 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7619 (tp30) REVERT: a 427 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.8111 (tptp) REVERT: a 590 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7625 (tm130) REVERT: a 745 GLU cc_start: 0.8125 (mp0) cc_final: 0.7786 (mp0) REVERT: a 761 GLU cc_start: 0.5913 (mt-10) cc_final: 0.5614 (mm-30) outliers start: 14 outliers final: 4 residues processed: 83 average time/residue: 0.6800 time to fit residues: 59.1069 Evaluate side-chains 79 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 103 VAL Chi-restraints excluded: chain a residue 336 THR Chi-restraints excluded: chain a residue 390 GLU Chi-restraints excluded: chain a residue 412 ARG Chi-restraints excluded: chain a residue 427 LYS Chi-restraints excluded: chain a residue 435 ARG Chi-restraints excluded: chain a residue 590 GLN Chi-restraints excluded: chain a residue 684 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 37 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 69 optimal weight: 0.2980 chunk 47 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 325 ASN ** a 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 482 HIS a 590 GLN a 685 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.172304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.132278 restraints weight = 7109.728| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.17 r_work: 0.3230 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6929 Z= 0.137 Angle : 0.494 4.799 9549 Z= 0.264 Chirality : 0.041 0.144 1068 Planarity : 0.004 0.039 1138 Dihedral : 14.799 141.347 1249 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.85 % Allowed : 11.13 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.30), residues: 758 helix: 2.38 (0.34), residues: 236 sheet: 0.75 (0.41), residues: 176 loop : -0.13 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG a 290 TYR 0.014 0.001 TYR a 380 PHE 0.013 0.001 PHE a 545 TRP 0.009 0.001 TRP a 136 HIS 0.003 0.001 HIS a 139 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 6929) covalent geometry : angle 0.49409 ( 9549) hydrogen bonds : bond 0.03718 ( 296) hydrogen bonds : angle 4.46581 ( 813) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: a 54 LYS cc_start: 0.8278 (mtpt) cc_final: 0.7275 (mptp) REVERT: a 276 ARG cc_start: 0.6635 (tpt90) cc_final: 0.6317 (tpt90) REVERT: a 328 ARG cc_start: 0.7770 (mmt180) cc_final: 0.7553 (mmt180) REVERT: a 361 ASN cc_start: 0.7898 (m-40) cc_final: 0.7300 (t0) REVERT: a 390 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7433 (tm-30) REVERT: a 412 ARG cc_start: 0.6863 (OUTLIER) cc_final: 0.6491 (tmm160) REVERT: a 417 LYS cc_start: 0.7676 (mppt) cc_final: 0.7344 (mppt) REVERT: a 424 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7638 (tp30) REVERT: a 745 GLU cc_start: 0.8185 (mp0) cc_final: 0.7841 (mp0) REVERT: a 761 GLU cc_start: 0.5928 (mt-10) cc_final: 0.5623 (mm-30) outliers start: 12 outliers final: 6 residues processed: 78 average time/residue: 0.7436 time to fit residues: 60.4630 Evaluate side-chains 75 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 103 VAL Chi-restraints excluded: chain a residue 158 VAL Chi-restraints excluded: chain a residue 336 THR Chi-restraints excluded: chain a residue 390 GLU Chi-restraints excluded: chain a residue 412 ARG Chi-restraints excluded: chain a residue 427 LYS Chi-restraints excluded: chain a residue 435 ARG Chi-restraints excluded: chain a residue 684 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 21 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 74 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 65 optimal weight: 0.0980 chunk 23 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 325 ASN ** a 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 482 HIS a 590 GLN a 685 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.172955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.132831 restraints weight = 7136.483| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.06 r_work: 0.3254 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6929 Z= 0.116 Angle : 0.479 4.918 9549 Z= 0.258 Chirality : 0.040 0.140 1068 Planarity : 0.004 0.036 1138 Dihedral : 14.805 141.559 1249 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.70 % Allowed : 11.28 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.30), residues: 758 helix: 2.44 (0.34), residues: 236 sheet: 0.77 (0.41), residues: 176 loop : -0.11 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG a 290 TYR 0.014 0.001 TYR a 380 PHE 0.014 0.001 PHE a 232 TRP 0.010 0.001 TRP a 570 HIS 0.003 0.001 HIS a 391 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 6929) covalent geometry : angle 0.47944 ( 9549) hydrogen bonds : bond 0.03523 ( 296) hydrogen bonds : angle 4.42193 ( 813) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: a 54 LYS cc_start: 0.8263 (mtpt) cc_final: 0.7260 (mptp) REVERT: a 276 ARG cc_start: 0.6619 (tpt90) cc_final: 0.6292 (tpt90) REVERT: a 328 ARG cc_start: 0.7765 (mmt180) cc_final: 0.7520 (mpt-90) REVERT: a 361 ASN cc_start: 0.7884 (m-40) cc_final: 0.7290 (t0) REVERT: a 390 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7428 (tm-30) REVERT: a 412 ARG cc_start: 0.6865 (OUTLIER) cc_final: 0.6505 (tmm160) REVERT: a 417 LYS cc_start: 0.7666 (mppt) cc_final: 0.7367 (mtmt) REVERT: a 424 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7629 (tp30) REVERT: a 745 GLU cc_start: 0.8117 (mp0) cc_final: 0.7794 (mp0) REVERT: a 761 GLU cc_start: 0.5901 (mt-10) cc_final: 0.5629 (mm-30) outliers start: 11 outliers final: 6 residues processed: 75 average time/residue: 0.6783 time to fit residues: 53.2585 Evaluate side-chains 74 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 103 VAL Chi-restraints excluded: chain a residue 158 VAL Chi-restraints excluded: chain a residue 336 THR Chi-restraints excluded: chain a residue 390 GLU Chi-restraints excluded: chain a residue 412 ARG Chi-restraints excluded: chain a residue 427 LYS Chi-restraints excluded: chain a residue 435 ARG Chi-restraints excluded: chain a residue 684 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/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-2.1rc2-6044/lib/python3.9/site-packages/iotbx/cli_parser.py", line 995, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1590, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1493, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1374, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.3844 > 50: distance: 70 - 90: 7.744 distance: 73 - 87: 21.514 distance: 83 - 87: 24.635 distance: 87 - 88: 40.550 distance: 88 - 89: 10.222 distance: 88 - 91: 13.837 distance: 89 - 90: 23.712 distance: 89 - 96: 21.056 distance: 91 - 92: 36.031 distance: 92 - 93: 11.980 distance: 93 - 94: 19.891 distance: 93 - 95: 19.809 distance: 96 - 97: 26.123 distance: 97 - 98: 18.363 distance: 97 - 100: 8.772 distance: 98 - 99: 19.919 distance: 98 - 104: 45.606 distance: 100 - 101: 17.951 distance: 101 - 102: 12.422 distance: 101 - 103: 19.279 distance: 104 - 105: 25.165 distance: 104 - 110: 16.286 distance: 105 - 106: 23.369 distance: 105 - 108: 23.086 distance: 106 - 107: 48.651 distance: 106 - 111: 21.867 distance: 108 - 109: 16.008 distance: 109 - 110: 9.842 distance: 111 - 112: 16.585 distance: 112 - 113: 25.309 distance: 112 - 115: 16.416 distance: 113 - 114: 14.590 distance: 113 - 119: 20.260 distance: 115 - 116: 41.446 distance: 116 - 117: 31.703 distance: 117 - 118: 46.807 distance: 119 - 120: 19.193 distance: 119 - 125: 11.677 distance: 120 - 121: 11.801 distance: 120 - 123: 14.294 distance: 121 - 122: 26.583 distance: 121 - 126: 26.216 distance: 123 - 124: 10.525 distance: 124 - 125: 26.238 distance: 126 - 127: 29.137 distance: 127 - 128: 33.645 distance: 128 - 129: 15.092 distance: 128 - 130: 30.996 distance: 130 - 131: 14.181 distance: 131 - 132: 23.330 distance: 131 - 134: 5.831 distance: 132 - 133: 29.611 distance: 132 - 136: 16.376 distance: 133 - 191: 20.807 distance: 134 - 135: 31.355 distance: 136 - 137: 24.473 distance: 137 - 138: 25.123 distance: 137 - 140: 13.059 distance: 138 - 139: 8.055 distance: 138 - 146: 25.577 distance: 140 - 141: 20.914 distance: 141 - 142: 15.340 distance: 141 - 143: 13.793 distance: 142 - 144: 9.651 distance: 143 - 145: 9.577 distance: 144 - 145: 8.266 distance: 146 - 147: 8.099 distance: 146 - 181: 10.485 distance: 147 - 148: 12.686 distance: 147 - 150: 11.705 distance: 148 - 149: 7.475 distance: 148 - 154: 14.636 distance: 149 - 178: 14.283 distance: 150 - 151: 11.520 distance: 151 - 152: 9.052 distance: 151 - 153: 13.138 distance: 154 - 155: 32.567 distance: 155 - 156: 9.290 distance: 155 - 158: 14.457 distance: 156 - 157: 22.262 distance: 156 - 162: 17.616 distance: 158 - 159: 29.458 distance: 158 - 160: 12.133 distance: 159 - 161: 25.803