Starting phenix.real_space_refine on Thu Jan 16 14:07:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xck_33123/01_2025/7xck_33123.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xck_33123/01_2025/7xck_33123.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xck_33123/01_2025/7xck_33123.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xck_33123/01_2025/7xck_33123.map" model { file = "/net/cci-nas-00/data/ceres_data/7xck_33123/01_2025/7xck_33123.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xck_33123/01_2025/7xck_33123.cif" } resolution = 2.5 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= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4868 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 3473 2.51 5 N 927 2.21 5 O 1067 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 5488 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1688 Classifications: {'peptide': 223} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 210} Chain breaks: 1 Chain: "B" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1615 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 200} Chain: "M" Number of atoms: 2147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2147 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 16, 'TRANS': 252} Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.28, per 1000 atoms: 1.14 Number of scatterers: 5488 At special positions: 0 Unit cell: (113.9, 61.64, 122.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 21 16.00 O 1067 8.00 N 927 7.00 C 3473 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 210 " distance=2.04 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 89 " distance=2.04 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS M 336 " - pdb=" SG CYS M 361 " distance=2.03 Simple disulfide: pdb=" SG CYS M 379 " - pdb=" SG CYS M 432 " distance=2.04 Simple disulfide: pdb=" SG CYS M 480 " - pdb=" SG CYS M 488 " distance=2.03 Simple disulfide: pdb=" SG CYS M 538 " - pdb=" SG CYS M 590 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " BETA1-6 " NAG C 1 " - " FUC C 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG C 1 " - " ASN M 343 " Time building additional restraints: 1.58 Conformation dependent library (CDL) restraints added in 833.8 milliseconds 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1302 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 14 sheets defined 9.7% alpha, 38.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.646A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.942A pdb=" N THR A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'B' and resid 80 through 84 removed outlier: 4.031A pdb=" N PHE B 84 " --> pdb=" O PRO B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 188 removed outlier: 3.542A pdb=" N LYS B 188 " --> pdb=" O ALA B 184 " (cutoff:3.500A) Processing helix chain 'M' and resid 338 through 343 Processing helix chain 'M' and resid 365 through 369 Processing helix chain 'M' and resid 383 through 390 removed outlier: 3.529A pdb=" N LEU M 387 " --> pdb=" O PRO M 384 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ASN M 388 " --> pdb=" O THR M 385 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU M 390 " --> pdb=" O LEU M 387 " (cutoff:3.500A) Processing helix chain 'M' and resid 403 through 410 removed outlier: 3.521A pdb=" N GLU M 406 " --> pdb=" O ARG M 403 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL M 407 " --> pdb=" O GLY M 404 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG M 408 " --> pdb=" O ASP M 405 " (cutoff:3.500A) Processing helix chain 'M' and resid 416 through 422 Processing helix chain 'M' and resid 438 through 443 removed outlier: 3.707A pdb=" N SER M 443 " --> pdb=" O ASN M 439 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.515A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TRP A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE A 34 " --> pdb=" O TRP A 50 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASN A 116 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.515A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TRP A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE A 34 " --> pdb=" O TRP A 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 134 through 138 removed outlier: 6.127A pdb=" N TYR A 190 " --> pdb=" O ASP A 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 134 through 138 removed outlier: 6.127A pdb=" N TYR A 190 " --> pdb=" O ASP A 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 165 through 168 Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.402A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU B 34 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N TYR B 50 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TRP B 36 " --> pdb=" O LEU B 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.402A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 116 through 118 removed outlier: 3.957A pdb=" N VAL B 133 " --> pdb=" O PHE B 118 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN B 138 " --> pdb=" O TYR B 173 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR B 173 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 145 through 149 Processing sheet with id=AB3, first strand: chain 'M' and resid 325 through 328 removed outlier: 5.842A pdb=" N ASP M 574 " --> pdb=" O ILE M 587 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY M 566 " --> pdb=" O ASP M 574 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 354 through 358 Processing sheet with id=AB5, first strand: chain 'M' and resid 452 through 454 209 hydrogen bonds defined for protein. 513 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.84 Time building geometry restraints manager: 1.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 948 1.32 - 1.45: 1605 1.45 - 1.58: 3044 1.58 - 1.71: 0 1.71 - 1.84: 24 Bond restraints: 5621 Sorted by residual: bond pdb=" C ALA M 344 " pdb=" N THR M 345 " ideal model delta sigma weight residual 1.335 1.278 0.057 1.25e-02 6.40e+03 2.05e+01 bond pdb=" CA ALA M 344 " pdb=" CB ALA M 344 " ideal model delta sigma weight residual 1.528 1.474 0.054 1.58e-02 4.01e+03 1.15e+01 bond pdb=" C ALA M 344 " pdb=" O ALA M 344 " ideal model delta sigma weight residual 1.235 1.201 0.034 1.20e-02 6.94e+03 8.18e+00 bond pdb=" C ASN M 343 " pdb=" O ASN M 343 " ideal model delta sigma weight residual 1.235 1.197 0.038 1.32e-02 5.74e+03 8.17e+00 bond pdb=" CA ALA M 344 " pdb=" C ALA M 344 " ideal model delta sigma weight residual 1.524 1.486 0.038 1.33e-02 5.65e+03 8.00e+00 ... (remaining 5616 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 7496 2.21 - 4.43: 120 4.43 - 6.64: 25 6.64 - 8.85: 2 8.85 - 11.07: 1 Bond angle restraints: 7644 Sorted by residual: angle pdb=" CA ASN M 334 " pdb=" C ASN M 334 " pdb=" O ASN M 334 " ideal model delta sigma weight residual 121.15 116.26 4.89 1.10e+00 8.26e-01 1.98e+01 angle pdb=" C VAL B 150 " pdb=" N ASP B 151 " pdb=" CA ASP B 151 " ideal model delta sigma weight residual 121.54 129.19 -7.65 1.91e+00 2.74e-01 1.60e+01 angle pdb=" C ASN M 343 " pdb=" CA ASN M 343 " pdb=" CB ASN M 343 " ideal model delta sigma weight residual 111.02 104.60 6.42 1.61e+00 3.86e-01 1.59e+01 angle pdb=" C PRO A 161 " pdb=" N GLU A 162 " pdb=" CA GLU A 162 " ideal model delta sigma weight residual 120.26 125.14 -4.88 1.34e+00 5.57e-01 1.33e+01 angle pdb=" C SER B 95 " pdb=" CA SER B 95 " pdb=" CB SER B 95 " ideal model delta sigma weight residual 115.89 111.20 4.69 1.32e+00 5.74e-01 1.26e+01 ... (remaining 7639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 3108 17.59 - 35.17: 228 35.17 - 52.76: 47 52.76 - 70.34: 5 70.34 - 87.93: 4 Dihedral angle restraints: 3392 sinusoidal: 1356 harmonic: 2036 Sorted by residual: dihedral pdb=" CB CYS A 154 " pdb=" SG CYS A 154 " pdb=" SG CYS A 210 " pdb=" CB CYS A 210 " ideal model delta sinusoidal sigma weight residual 93.00 162.64 -69.64 1 1.00e+01 1.00e-02 6.26e+01 dihedral pdb=" CB CYS M 538 " pdb=" SG CYS M 538 " pdb=" SG CYS M 590 " pdb=" CB CYS M 590 " ideal model delta sinusoidal sigma weight residual -86.00 -38.35 -47.65 1 1.00e+01 1.00e-02 3.13e+01 dihedral pdb=" CB CYS M 379 " pdb=" SG CYS M 379 " pdb=" SG CYS M 432 " pdb=" CB CYS M 432 " ideal model delta sinusoidal sigma weight residual -86.00 -51.56 -34.44 1 1.00e+01 1.00e-02 1.68e+01 ... (remaining 3389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.142: 855 0.142 - 0.284: 2 0.284 - 0.425: 0 0.425 - 0.567: 0 0.567 - 0.709: 1 Chirality restraints: 858 Sorted by residual: chirality pdb=" C1 FUC C 3 " pdb=" O6 NAG C 1 " pdb=" C2 FUC C 3 " pdb=" O5 FUC C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 2.19e+01 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN M 343 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.26e+01 chirality pdb=" CA VAL A 37 " pdb=" N VAL A 37 " pdb=" C VAL A 37 " pdb=" CB VAL A 37 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.69e-01 ... (remaining 855 not shown) Planarity restraints: 982 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " -0.045 2.00e-02 2.50e+03 3.72e-02 1.73e+01 pdb=" C7 NAG C 1 " 0.011 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " -0.034 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " 0.060 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 2 " 0.041 2.00e-02 2.50e+03 3.36e-02 1.41e+01 pdb=" C7 NAG C 2 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG C 2 " 0.032 2.00e-02 2.50e+03 pdb=" N2 NAG C 2 " -0.052 2.00e-02 2.50e+03 pdb=" O7 NAG C 2 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA M 520 " 0.043 5.00e-02 4.00e+02 6.51e-02 6.78e+00 pdb=" N PRO M 521 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO M 521 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO M 521 " 0.036 5.00e-02 4.00e+02 ... (remaining 979 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 246 2.72 - 3.27: 5007 3.27 - 3.81: 8362 3.81 - 4.36: 10652 4.36 - 4.90: 18600 Nonbonded interactions: 42867 Sorted by model distance: nonbonded pdb=" OH TYR M 369 " pdb=" O PRO M 384 " model vdw 2.179 3.040 nonbonded pdb=" OG SER B 64 " pdb=" OG1 THR B 75 " model vdw 2.198 3.040 nonbonded pdb=" OG1 THR A 149 " pdb=" O VAL A 198 " model vdw 2.228 3.040 nonbonded pdb=" OE1 GLU B 105 " pdb=" OH TYR B 173 " model vdw 2.296 3.040 nonbonded pdb=" O ASP M 442 " pdb=" ND2 ASN M 448 " model vdw 2.307 3.120 ... (remaining 42862 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: 9.260 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 19.610 Find NCS groups from input model: 0.070 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: 0.000 Load rotamer database and sin/cos tables:11.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 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 : 0.004 0.057 5621 Z= 0.251 Angle : 0.713 11.067 7644 Z= 0.389 Chirality : 0.052 0.709 858 Planarity : 0.006 0.065 981 Dihedral : 12.630 87.930 2066 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.60 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.89 (0.32), residues: 696 helix: -3.99 (0.85), residues: 20 sheet: 0.21 (0.33), residues: 271 loop : -0.98 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 436 HIS 0.004 0.001 HIS M 519 PHE 0.012 0.001 PHE M 374 TYR 0.007 0.001 TYR A 159 ARG 0.002 0.000 ARG M 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.614 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 1.5003 time to fit residues: 107.8793 Evaluate side-chains 57 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 17 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 0.0060 chunk 20 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 GLN B 189 HIS M 417 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.183251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.118135 restraints weight = 6045.256| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.52 r_work: 0.3278 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.0816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5621 Z= 0.186 Angle : 0.590 8.922 7644 Z= 0.305 Chirality : 0.046 0.138 858 Planarity : 0.005 0.060 981 Dihedral : 4.950 20.267 823 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.47 % Allowed : 5.92 % Favored : 91.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.84 (0.33), residues: 696 helix: -4.43 (0.54), residues: 26 sheet: 0.37 (0.33), residues: 268 loop : -0.94 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 47 HIS 0.004 0.001 HIS B 92 PHE 0.012 0.001 PHE M 377 TYR 0.008 0.001 TYR M 369 ARG 0.004 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: A 43 GLN cc_start: 0.7923 (mm-40) cc_final: 0.7309 (mp10) REVERT: A 82 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7647 (tp30) REVERT: B 117 ILE cc_start: 0.6493 (tt) cc_final: 0.6053 (mm) REVERT: M 357 ARG cc_start: 0.8712 (ttp-170) cc_final: 0.8300 (ttp80) REVERT: M 405 ASP cc_start: 0.7830 (p0) cc_final: 0.7589 (p0) REVERT: M 586 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7948 (m-30) outliers start: 15 outliers final: 5 residues processed: 70 average time/residue: 1.3716 time to fit residues: 100.2236 Evaluate side-chains 64 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain M residue 332 ILE Chi-restraints excluded: chain M residue 553 THR Chi-restraints excluded: chain M residue 586 ASP Chi-restraints excluded: chain M residue 588 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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: 59.5007 > 50: distance: 37 - 86: 24.307 distance: 40 - 83: 30.086 distance: 50 - 71: 19.894 distance: 53 - 68: 7.978 distance: 64 - 68: 9.387 distance: 68 - 69: 11.033 distance: 69 - 70: 6.562 distance: 69 - 72: 12.230 distance: 70 - 71: 11.883 distance: 70 - 76: 13.696 distance: 72 - 73: 12.042 distance: 73 - 74: 12.189 distance: 73 - 75: 4.360 distance: 76 - 77: 5.432 distance: 76 - 195: 20.828 distance: 77 - 78: 9.748 distance: 77 - 80: 6.947 distance: 78 - 79: 14.778 distance: 78 - 83: 9.835 distance: 79 - 192: 9.536 distance: 80 - 81: 12.928 distance: 80 - 82: 7.218 distance: 83 - 84: 14.615 distance: 84 - 85: 7.027 distance: 84 - 87: 13.326 distance: 85 - 86: 8.454 distance: 87 - 88: 17.338 distance: 88 - 89: 18.695 distance: 89 - 90: 24.309 distance: 90 - 91: 6.859 distance: 92 - 93: 10.011 distance: 92 - 177: 24.798 distance: 93 - 94: 4.472 distance: 93 - 96: 19.526 distance: 94 - 95: 9.199 distance: 94 - 100: 7.351 distance: 96 - 97: 12.204 distance: 97 - 98: 12.300 distance: 97 - 99: 28.321 distance: 100 - 101: 17.461 distance: 101 - 102: 16.792 distance: 101 - 104: 37.796 distance: 102 - 103: 17.017 distance: 102 - 112: 12.886 distance: 104 - 105: 6.086 distance: 105 - 106: 18.812 distance: 105 - 107: 7.862 distance: 106 - 108: 13.723 distance: 107 - 109: 13.708 distance: 109 - 110: 13.610 distance: 110 - 111: 11.679 distance: 112 - 113: 14.330 distance: 113 - 114: 6.975 distance: 113 - 116: 15.130 distance: 114 - 115: 19.929 distance: 114 - 123: 43.619 distance: 116 - 117: 4.760 distance: 117 - 118: 3.815 distance: 117 - 119: 12.233 distance: 118 - 120: 9.880 distance: 119 - 121: 12.239 distance: 120 - 122: 14.341 distance: 121 - 122: 5.806 distance: 123 - 124: 19.182 distance: 123 - 129: 9.270 distance: 124 - 125: 6.795 distance: 124 - 127: 10.841 distance: 125 - 126: 20.038 distance: 125 - 130: 7.824 distance: 127 - 128: 22.748 distance: 128 - 129: 15.037 distance: 130 - 131: 12.234 distance: 131 - 132: 7.221 distance: 131 - 134: 39.719 distance: 132 - 133: 25.718 distance: 132 - 139: 19.034 distance: 134 - 135: 11.145 distance: 135 - 136: 25.119 distance: 136 - 137: 18.803 distance: 136 - 138: 39.224 distance: 139 - 140: 7.001 distance: 139 - 145: 21.697 distance: 140 - 141: 7.245 distance: 140 - 143: 8.668 distance: 141 - 142: 9.835 distance: 141 - 146: 13.493 distance: 143 - 144: 18.858 distance: 144 - 145: 21.086 distance: 146 - 147: 14.324 distance: 147 - 148: 16.116 distance: 147 - 150: 14.812 distance: 148 - 149: 18.781 distance: 148 - 153: 17.707 distance: 150 - 151: 17.025 distance: 150 - 152: 18.360