Starting phenix.real_space_refine on Tue Mar 11 15:32:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c9y_45376/03_2025/9c9y_45376_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c9y_45376/03_2025/9c9y_45376.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c9y_45376/03_2025/9c9y_45376.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c9y_45376/03_2025/9c9y_45376.map" model { file = "/net/cci-nas-00/data/ceres_data/9c9y_45376/03_2025/9c9y_45376_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c9y_45376/03_2025/9c9y_45376_neut.cif" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.001 sd= 0.020 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 Mn 2 7.51 5 P 8 5.49 5 S 39 5.16 5 C 3908 2.51 5 N 1077 2.21 5 O 1191 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6225 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4840 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 30, 'TRANS': 581} Chain: "B" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1219 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "C" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 164 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.62, per 1000 atoms: 0.74 Number of scatterers: 6225 At special positions: 0 Unit cell: (69.72, 87.15, 136.12, 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) Mn 2 24.99 S 39 16.00 P 8 15.00 O 1191 8.00 N 1077 7.00 C 3908 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: 1.56 Conformation dependent library (CDL) restraints added in 865.6 milliseconds 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1442 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 7 sheets defined 40.9% alpha, 20.8% beta 0 base pairs and 3 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'A' and resid 10 through 23 Processing helix chain 'A' and resid 77 through 82 removed outlier: 3.622A pdb=" N PHE A 82 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 107 Processing helix chain 'A' and resid 119 through 134 removed outlier: 4.160A pdb=" N GLU A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ASN A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ILE A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 166 Processing helix chain 'A' and resid 171 through 200 removed outlier: 3.743A pdb=" N SER A 177 " --> pdb=" O ASN A 173 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG A 194 " --> pdb=" O CYS A 190 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 234 removed outlier: 3.632A pdb=" N CYS A 225 " --> pdb=" O THR A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 276 Processing helix chain 'A' and resid 302 through 314 Processing helix chain 'A' and resid 317 through 332 Processing helix chain 'A' and resid 349 through 357 removed outlier: 3.832A pdb=" N GLN A 357 " --> pdb=" O SER A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 374 Processing helix chain 'A' and resid 403 through 419 removed outlier: 3.687A pdb=" N TYR A 411 " --> pdb=" O ARG A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 455 Processing helix chain 'A' and resid 456 through 460 Processing helix chain 'A' and resid 495 through 507 removed outlier: 3.725A pdb=" N LYS A 505 " --> pdb=" O THR A 501 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 524 Processing helix chain 'A' and resid 538 through 552 removed outlier: 3.750A pdb=" N LYS A 550 " --> pdb=" O HIS A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 574 removed outlier: 4.193A pdb=" N SER A 562 " --> pdb=" O PRO A 558 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU A 570 " --> pdb=" O LYS A 566 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ILE A 571 " --> pdb=" O GLN A 567 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 599 removed outlier: 3.954A pdb=" N HIS A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE A 589 " --> pdb=" O THR A 585 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP A 598 " --> pdb=" O HIS A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 605 Processing helix chain 'A' and resid 606 through 610 removed outlier: 3.895A pdb=" N VAL A 609 " --> pdb=" O LEU A 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 13 removed outlier: 3.664A pdb=" N ALA B 7 " --> pdb=" O GLN B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 25 Processing helix chain 'B' and resid 32 through 41 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 5.780A pdb=" N SER A 37 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N SER A 56 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N THR A 3 " --> pdb=" O TYR A 111 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N VAL A 113 " --> pdb=" O THR A 3 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU A 5 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N TRP A 115 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL A 7 " --> pdb=" O TRP A 115 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE A 112 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 66 Processing sheet with id=AA3, first strand: chain 'A' and resid 253 through 256 removed outlier: 7.037A pdb=" N ARG A 253 " --> pdb=" O THR A 249 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL A 242 " --> pdb=" O MET A 483 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N MET A 483 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLN A 244 " --> pdb=" O VAL A 481 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N VAL A 481 " --> pdb=" O GLN A 244 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LYS A 246 " --> pdb=" O GLY A 479 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N ASP A 250 " --> pdb=" O ALA A 475 " (cutoff:3.500A) removed outlier: 13.734A pdb=" N ALA A 475 " --> pdb=" O ASP A 250 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N SER A 432 " --> pdb=" O GLU A 286 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N THR A 288 " --> pdb=" O THR A 430 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N THR A 430 " --> pdb=" O THR A 288 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LYS A 425 " --> pdb=" O LEU A 448 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 253 through 256 removed outlier: 7.037A pdb=" N ARG A 253 " --> pdb=" O THR A 249 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL A 242 " --> pdb=" O MET A 483 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N MET A 483 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLN A 244 " --> pdb=" O VAL A 481 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N VAL A 481 " --> pdb=" O GLN A 244 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LYS A 246 " --> pdb=" O GLY A 479 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N ASP A 250 " --> pdb=" O ALA A 475 " (cutoff:3.500A) removed outlier: 13.734A pdb=" N ALA A 475 " --> pdb=" O ASP A 250 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N SER A 432 " --> pdb=" O GLU A 286 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N THR A 288 " --> pdb=" O THR A 430 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N THR A 430 " --> pdb=" O THR A 288 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N CYS A 424 " --> pdb=" O LYS A 295 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A 291 " --> pdb=" O GLN A 428 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 527 through 530 removed outlier: 3.679A pdb=" N ARG A 534 " --> pdb=" O GLU A 530 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 65 through 66 Processing sheet with id=AA7, first strand: chain 'B' and resid 139 through 141 removed outlier: 3.884A pdb=" N ILE B 104 " --> pdb=" O ASP B 101 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ARG B 96 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ILE B 76 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLN B 98 " --> pdb=" O GLN B 74 " (cutoff:3.500A) 276 hydrogen bonds defined for protein. 786 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 3 stacking parallelities Total time for adding SS restraints: 1.88 Time building geometry restraints manager: 1.86 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: 1997 1.34 - 1.45: 883 1.45 - 1.57: 3413 1.57 - 1.69: 13 1.69 - 1.81: 61 Bond restraints: 6367 Sorted by residual: bond pdb=" O3' DT C 1 " pdb=" P DA C 2 " ideal model delta sigma weight residual 1.607 1.556 0.051 1.50e-02 4.44e+03 1.15e+01 bond pdb=" O3' DA C 2 " pdb=" P DA C 3 " ideal model delta sigma weight residual 1.607 1.559 0.048 1.50e-02 4.44e+03 1.03e+01 bond pdb=" O3' DC C 0 " pdb=" P DT C 1 " ideal model delta sigma weight residual 1.607 1.572 0.035 1.50e-02 4.44e+03 5.34e+00 bond pdb=" C TRP A 73 " pdb=" N ASP A 74 " ideal model delta sigma weight residual 1.332 1.303 0.029 1.41e-02 5.03e+03 4.32e+00 bond pdb=" CG LEU A 114 " pdb=" CD1 LEU A 114 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.90e+00 ... (remaining 6362 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 8362 1.58 - 3.15: 229 3.15 - 4.73: 34 4.73 - 6.31: 18 6.31 - 7.89: 4 Bond angle restraints: 8647 Sorted by residual: angle pdb=" C4' DA C 2 " pdb=" C3' DA C 2 " pdb=" O3' DA C 2 " ideal model delta sigma weight residual 110.00 104.30 5.70 1.50e+00 4.44e-01 1.45e+01 angle pdb=" C3' DT C 6 " pdb=" C2' DT C 6 " pdb=" C1' DT C 6 " ideal model delta sigma weight residual 101.60 105.56 -3.96 1.50e+00 4.44e-01 6.97e+00 angle pdb=" CB MET A 272 " pdb=" CG MET A 272 " pdb=" SD MET A 272 " ideal model delta sigma weight residual 112.70 120.59 -7.89 3.00e+00 1.11e-01 6.91e+00 angle pdb=" C ALA A 553 " pdb=" N GLU A 554 " pdb=" CA GLU A 554 " ideal model delta sigma weight residual 121.58 116.62 4.96 1.95e+00 2.63e-01 6.48e+00 angle pdb=" N SER B 27 " pdb=" CA SER B 27 " pdb=" C SER B 27 " ideal model delta sigma weight residual 109.81 115.40 -5.59 2.21e+00 2.05e-01 6.40e+00 ... (remaining 8642 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.02: 3645 29.02 - 58.04: 196 58.04 - 87.06: 14 87.06 - 116.08: 0 116.08 - 145.10: 1 Dihedral angle restraints: 3856 sinusoidal: 1622 harmonic: 2234 Sorted by residual: dihedral pdb=" CD ARG A 149 " pdb=" NE ARG A 149 " pdb=" CZ ARG A 149 " pdb=" NH1 ARG A 149 " ideal model delta sinusoidal sigma weight residual 0.00 71.03 -71.03 1 1.00e+01 1.00e-02 6.48e+01 dihedral pdb=" CG ARG B 77 " pdb=" CD ARG B 77 " pdb=" NE ARG B 77 " pdb=" CZ ARG B 77 " ideal model delta sinusoidal sigma weight residual -90.00 -32.53 -57.47 2 1.50e+01 4.44e-03 1.52e+01 dihedral pdb=" C4' DA C -1 " pdb=" C3' DA C -1 " pdb=" O3' DA C -1 " pdb=" P DC C 0 " ideal model delta sinusoidal sigma weight residual 220.00 74.90 145.10 1 3.50e+01 8.16e-04 1.43e+01 ... (remaining 3853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 572 0.033 - 0.066: 274 0.066 - 0.100: 84 0.100 - 0.133: 37 0.133 - 0.166: 3 Chirality restraints: 970 Sorted by residual: chirality pdb=" CB ILE A 155 " pdb=" CA ILE A 155 " pdb=" CG1 ILE A 155 " pdb=" CG2 ILE A 155 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.17 2.00e-01 2.50e+01 6.90e-01 chirality pdb=" CA ILE A 435 " pdb=" N ILE A 435 " pdb=" C ILE A 435 " pdb=" CB ILE A 435 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.49e-01 chirality pdb=" CA THR A 219 " pdb=" N THR A 219 " pdb=" C THR A 219 " pdb=" CB THR A 219 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.55e-01 ... (remaining 967 not shown) Planarity restraints: 1090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 149 " 1.040 9.50e-02 1.11e+02 4.66e-01 1.31e+02 pdb=" NE ARG A 149 " -0.062 2.00e-02 2.50e+03 pdb=" CZ ARG A 149 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 149 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 149 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 27 " -0.038 5.00e-02 4.00e+02 5.77e-02 5.33e+00 pdb=" N PRO B 28 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO B 28 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 28 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 476 " -0.037 5.00e-02 4.00e+02 5.59e-02 5.01e+00 pdb=" N PRO A 477 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 477 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 477 " -0.031 5.00e-02 4.00e+02 ... (remaining 1087 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 51 2.61 - 3.18: 5211 3.18 - 3.76: 8887 3.76 - 4.33: 11637 4.33 - 4.90: 19671 Nonbonded interactions: 45457 Sorted by model distance: nonbonded pdb=" OD2 ASP A 511 " pdb="MN MN A 702 " model vdw 2.041 2.320 nonbonded pdb=" OP1 DA C 5 " pdb="MN MN A 701 " model vdw 2.114 2.320 nonbonded pdb=" OD2 ASP A 117 " pdb="MN MN A 701 " model vdw 2.120 2.320 nonbonded pdb=" OE2 GLU A 340 " pdb="MN MN A 702 " model vdw 2.158 2.320 nonbonded pdb=" O ALA A 18 " pdb=" OG SER A 22 " model vdw 2.185 3.040 ... (remaining 45452 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: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 20.330 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 6367 Z= 0.355 Angle : 0.664 7.886 8647 Z= 0.343 Chirality : 0.044 0.166 970 Planarity : 0.015 0.466 1090 Dihedral : 16.017 145.098 2414 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.98 % Favored : 93.89 % Rotamer: Outliers : 0.15 % Allowed : 0.60 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.31), residues: 769 helix: 1.05 (0.31), residues: 296 sheet: 0.25 (0.44), residues: 157 loop : -1.14 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 73 HIS 0.003 0.001 HIS B 156 PHE 0.014 0.002 PHE A 200 TYR 0.011 0.001 TYR A 549 ARG 0.004 0.000 ARG A 369 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 228 time to evaluate : 0.662 Fit side-chains REVERT: A 19 LYS cc_start: 0.8434 (tttp) cc_final: 0.8115 (tttp) REVERT: A 109 CYS cc_start: 0.7564 (m) cc_final: 0.7163 (m) REVERT: A 119 ASP cc_start: 0.6978 (p0) cc_final: 0.6753 (p0) REVERT: A 128 GLU cc_start: 0.7105 (tm-30) cc_final: 0.6850 (tm-30) REVERT: A 226 VAL cc_start: 0.7580 (m) cc_final: 0.7362 (t) REVERT: A 246 LYS cc_start: 0.8562 (ptpt) cc_final: 0.8300 (ptpt) REVERT: A 282 GLU cc_start: 0.7338 (mm-30) cc_final: 0.7117 (mm-30) REVERT: A 393 MET cc_start: 0.8285 (mtp) cc_final: 0.7919 (mtp) REVERT: A 511 ASP cc_start: 0.6125 (p0) cc_final: 0.5916 (p0) REVERT: A 566 LYS cc_start: 0.8167 (ttpp) cc_final: 0.7929 (ttpt) REVERT: B 32 ASN cc_start: 0.7825 (t0) cc_final: 0.7175 (t0) REVERT: B 95 LEU cc_start: 0.8416 (mm) cc_final: 0.7996 (mp) outliers start: 1 outliers final: 0 residues processed: 229 average time/residue: 0.2286 time to fit residues: 65.1470 Evaluate side-chains 209 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.111981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.099339 restraints weight = 9702.429| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.60 r_work: 0.3121 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6367 Z= 0.280 Angle : 0.618 8.376 8647 Z= 0.310 Chirality : 0.043 0.179 970 Planarity : 0.004 0.046 1090 Dihedral : 10.660 140.493 926 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.20 % Allowed : 13.77 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.31), residues: 769 helix: 1.12 (0.31), residues: 296 sheet: 0.35 (0.45), residues: 151 loop : -1.19 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 406 HIS 0.006 0.001 HIS A 517 PHE 0.015 0.001 PHE A 433 TYR 0.011 0.001 TYR A 329 ARG 0.005 0.000 ARG B 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 219 time to evaluate : 0.647 Fit side-chains REVERT: A 19 LYS cc_start: 0.8584 (tttp) cc_final: 0.8225 (ttmm) REVERT: A 26 LEU cc_start: 0.7827 (mp) cc_final: 0.7626 (mt) REVERT: A 65 ASP cc_start: 0.7669 (t0) cc_final: 0.7458 (t0) REVERT: A 109 CYS cc_start: 0.7893 (m) cc_final: 0.7484 (m) REVERT: A 119 ASP cc_start: 0.7343 (p0) cc_final: 0.7141 (p0) REVERT: A 128 GLU cc_start: 0.7463 (tm-30) cc_final: 0.7061 (tm-30) REVERT: A 246 LYS cc_start: 0.8602 (ptpt) cc_final: 0.8352 (ptpt) REVERT: A 272 MET cc_start: 0.8110 (tmm) cc_final: 0.7818 (tmm) REVERT: A 282 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7384 (mm-30) REVERT: A 357 GLN cc_start: 0.8237 (mt0) cc_final: 0.7985 (mt0) REVERT: A 386 ASP cc_start: 0.7486 (m-30) cc_final: 0.7085 (m-30) REVERT: A 393 MET cc_start: 0.8530 (mtp) cc_final: 0.8140 (mtp) REVERT: A 423 ASP cc_start: 0.8054 (m-30) cc_final: 0.7768 (m-30) REVERT: A 464 GLU cc_start: 0.7467 (pm20) cc_final: 0.7196 (mp0) REVERT: A 474 ASP cc_start: 0.7511 (m-30) cc_final: 0.7275 (m-30) REVERT: A 480 GLU cc_start: 0.7322 (tm-30) cc_final: 0.6910 (tm-30) REVERT: A 566 LYS cc_start: 0.8281 (ttpp) cc_final: 0.8052 (ttpt) REVERT: B 32 ASN cc_start: 0.7990 (t0) cc_final: 0.7348 (t0) REVERT: B 61 LYS cc_start: 0.8075 (pttm) cc_final: 0.7862 (pttm) REVERT: B 136 LYS cc_start: 0.7746 (tptt) cc_final: 0.7159 (tptt) outliers start: 8 outliers final: 6 residues processed: 221 average time/residue: 0.2190 time to fit residues: 60.5499 Evaluate side-chains 219 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 213 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 442 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 16 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.111740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.098887 restraints weight = 9791.848| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.64 r_work: 0.3108 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6367 Z= 0.273 Angle : 0.592 8.664 8647 Z= 0.296 Chirality : 0.043 0.178 970 Planarity : 0.004 0.045 1090 Dihedral : 10.583 137.186 926 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.40 % Allowed : 16.77 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.31), residues: 769 helix: 1.12 (0.31), residues: 296 sheet: 0.36 (0.45), residues: 149 loop : -1.21 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 406 HIS 0.004 0.001 HIS A 517 PHE 0.012 0.001 PHE A 433 TYR 0.015 0.001 TYR A 41 ARG 0.004 0.000 ARG B 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 215 time to evaluate : 0.716 Fit side-chains REVERT: A 19 LYS cc_start: 0.8602 (tttp) cc_final: 0.8228 (ttmm) REVERT: A 109 CYS cc_start: 0.7880 (m) cc_final: 0.7471 (m) REVERT: A 119 ASP cc_start: 0.7324 (p0) cc_final: 0.7110 (p0) REVERT: A 128 GLU cc_start: 0.7455 (tm-30) cc_final: 0.7171 (tm-30) REVERT: A 246 LYS cc_start: 0.8610 (ptpt) cc_final: 0.8341 (ptpt) REVERT: A 272 MET cc_start: 0.8122 (tmm) cc_final: 0.7840 (tmm) REVERT: A 282 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7411 (mm-30) REVERT: A 357 GLN cc_start: 0.8252 (mt0) cc_final: 0.7997 (mt0) REVERT: A 377 ARG cc_start: 0.7678 (mmm160) cc_final: 0.7382 (mmm160) REVERT: A 393 MET cc_start: 0.8549 (mtp) cc_final: 0.8125 (mtp) REVERT: A 423 ASP cc_start: 0.8060 (m-30) cc_final: 0.7771 (m-30) REVERT: A 464 GLU cc_start: 0.7399 (pm20) cc_final: 0.7121 (mp0) REVERT: A 474 ASP cc_start: 0.7531 (m-30) cc_final: 0.7276 (m-30) REVERT: A 480 GLU cc_start: 0.7336 (tm-30) cc_final: 0.6929 (tm-30) REVERT: B 32 ASN cc_start: 0.7927 (t0) cc_final: 0.7304 (t0) REVERT: B 136 LYS cc_start: 0.7725 (tptt) cc_final: 0.7161 (tptt) outliers start: 16 outliers final: 9 residues processed: 221 average time/residue: 0.2293 time to fit residues: 63.6861 Evaluate side-chains 219 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 210 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 154 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.5833 > 50: distance: 71 - 111: 26.619 distance: 106 - 111: 23.768 distance: 111 - 112: 33.861 distance: 112 - 113: 14.755 distance: 113 - 114: 19.610 distance: 113 - 115: 25.493 distance: 115 - 116: 12.027 distance: 116 - 117: 51.032 distance: 116 - 119: 10.736 distance: 117 - 118: 56.843 distance: 117 - 124: 38.983 distance: 119 - 120: 41.632 distance: 120 - 121: 15.633 distance: 121 - 122: 31.356 distance: 124 - 125: 41.473 distance: 125 - 126: 58.099 distance: 125 - 128: 46.199 distance: 126 - 127: 55.358 distance: 126 - 131: 63.583 distance: 128 - 129: 40.076 distance: 128 - 130: 46.287 distance: 131 - 132: 18.718 distance: 132 - 133: 33.262 distance: 132 - 135: 43.118 distance: 133 - 134: 14.703 distance: 133 - 140: 11.639 distance: 135 - 136: 39.855 distance: 136 - 137: 7.692 distance: 137 - 138: 35.438 distance: 138 - 139: 23.389 distance: 141 - 142: 40.871 distance: 141 - 144: 41.177 distance: 142 - 148: 53.588 distance: 144 - 145: 13.501 distance: 145 - 146: 43.212 distance: 146 - 147: 39.506 distance: 148 - 149: 55.639 distance: 149 - 150: 52.645 distance: 149 - 152: 29.341 distance: 150 - 151: 41.120 distance: 150 - 156: 32.030 distance: 152 - 153: 33.339 distance: 153 - 154: 12.753 distance: 153 - 155: 45.233 distance: 156 - 157: 22.384 distance: 157 - 158: 40.606 distance: 157 - 160: 9.198 distance: 158 - 159: 39.162 distance: 158 - 165: 62.078 distance: 160 - 161: 36.483 distance: 161 - 162: 32.676 distance: 162 - 163: 27.304 distance: 162 - 164: 33.109 distance: 165 - 166: 36.788 distance: 166 - 167: 47.228 distance: 166 - 169: 41.864 distance: 167 - 168: 42.896 distance: 167 - 174: 53.636 distance: 169 - 170: 26.362 distance: 170 - 171: 23.669 distance: 171 - 172: 6.071 distance: 174 - 175: 44.776 distance: 175 - 176: 44.481 distance: 175 - 178: 42.831 distance: 176 - 177: 27.892 distance: 176 - 183: 55.081 distance: 178 - 179: 18.099 distance: 179 - 180: 19.140 distance: 180 - 181: 27.031 distance: 180 - 182: 40.300 distance: 183 - 184: 53.902 distance: 184 - 185: 12.340 distance: 184 - 187: 34.851 distance: 185 - 186: 44.114 distance: 185 - 190: 23.686 distance: 187 - 188: 28.661 distance: 187 - 189: 22.437