Starting phenix.real_space_refine on Thu Jun 5 23:13:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7whz_32516/06_2025/7whz_32516.cif Found real_map, /net/cci-nas-00/data/ceres_data/7whz_32516/06_2025/7whz_32516.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7whz_32516/06_2025/7whz_32516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7whz_32516/06_2025/7whz_32516.map" model { file = "/net/cci-nas-00/data/ceres_data/7whz_32516/06_2025/7whz_32516.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7whz_32516/06_2025/7whz_32516.cif" } resolution = 3.42 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= -0.000 sd= 0.015 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: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 4288 2.51 5 N 1142 2.21 5 O 1350 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 6810 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 11, 'TRANS': 182} Chain: "B" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 949 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "C" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 929 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "D" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "E" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 830 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 935 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 800 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.80, per 1000 atoms: 0.85 Number of scatterers: 6810 At special positions: 0 Unit cell: (81.69, 94.916, 119.812, 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 30 16.00 O 1350 8.00 N 1142 7.00 C 4288 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.02 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " 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 NAG-ASN " NAG A 601 " - " ASN A 343 " Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 986.5 milliseconds 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1602 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 23 sheets defined 2.6% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.578A pdb=" N GLU A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.735A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.610A pdb=" N ASP C 90 " --> pdb=" O ARG C 87 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA C 91 " --> pdb=" O VAL C 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.576A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 6 removed outlier: 3.555A pdb=" N SER B 25 " --> pdb=" O GLN B 3 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL B 5 " --> pdb=" O ALA B 23 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 12 removed outlier: 6.538A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.988A pdb=" N SER C 21 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU C 18 " --> pdb=" O MET C 83 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU C 81 " --> pdb=" O LEU C 20 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 12 Processing sheet with id=AA8, first strand: chain 'C' and resid 58 through 60 removed outlier: 3.668A pdb=" N TYR C 59 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL C 48 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N HIS C 35 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N CYS C 96 " --> pdb=" O TRP C 112 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N TRP C 112 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS C 98 " --> pdb=" O ASP C 110 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 4 through 7 removed outlier: 6.051A pdb=" N THR D 69 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR D 72 " --> pdb=" O SER D 65 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.737A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.737A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN D 90 " --> pdb=" O SER D 97 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 5 through 7 Processing sheet with id=AB4, first strand: chain 'E' and resid 10 through 12 Processing sheet with id=AB5, first strand: chain 'E' and resid 45 through 46 Processing sheet with id=AB6, first strand: chain 'E' and resid 48 through 49 Processing sheet with id=AB7, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AB8, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.699A pdb=" N GLU H 10 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA H 92 " --> pdb=" O VAL H 119 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.568A pdb=" N ASN H 59 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 68 through 69 removed outlier: 3.609A pdb=" N THR H 69 " --> pdb=" O ASP H 82 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 72 through 73 removed outlier: 3.524A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 17 through 23 removed outlier: 3.503A pdb=" N SER L 67 " --> pdb=" O SER L 74 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 36 through 40 Processing sheet with id=AC5, first strand: chain 'L' and resid 36 through 40 163 hydrogen bonds defined for protein. 381 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: 1.92 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2184 1.35 - 1.47: 1977 1.47 - 1.60: 2773 1.60 - 1.73: 0 1.73 - 1.86: 40 Bond restraints: 6974 Sorted by residual: bond pdb=" C LYS L 106 " pdb=" O LYS L 106 " ideal model delta sigma weight residual 1.235 1.273 -0.038 1.13e-02 7.83e+03 1.13e+01 bond pdb=" CA THR H 117 " pdb=" CB THR H 117 " ideal model delta sigma weight residual 1.527 1.450 0.078 2.48e-02 1.63e+03 9.81e+00 bond pdb=" CA TYR D 87 " pdb=" C TYR D 87 " ideal model delta sigma weight residual 1.526 1.496 0.029 1.36e-02 5.41e+03 4.67e+00 bond pdb=" CB VAL B 50 " pdb=" CG2 VAL B 50 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.75e+00 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.49e+00 ... (remaining 6969 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.45: 9394 3.45 - 6.89: 69 6.89 - 10.34: 10 10.34 - 13.78: 3 13.78 - 17.23: 1 Bond angle restraints: 9477 Sorted by residual: angle pdb=" N CYS A 432 " pdb=" CA CYS A 432 " pdb=" C CYS A 432 " ideal model delta sigma weight residual 110.17 121.04 -10.87 1.61e+00 3.86e-01 4.56e+01 angle pdb=" N CYS A 391 " pdb=" CA CYS A 391 " pdb=" C CYS A 391 " ideal model delta sigma weight residual 109.95 120.55 -10.60 1.59e+00 3.96e-01 4.45e+01 angle pdb=" N ASN A 394 " pdb=" CA ASN A 394 " pdb=" C ASN A 394 " ideal model delta sigma weight residual 108.99 117.30 -8.31 1.57e+00 4.06e-01 2.80e+01 angle pdb=" C GLU E 50 " pdb=" N THR E 51 " pdb=" CA THR E 51 " ideal model delta sigma weight residual 121.54 131.51 -9.97 1.91e+00 2.74e-01 2.73e+01 angle pdb=" N LYS L 106 " pdb=" CA LYS L 106 " pdb=" C LYS L 106 " ideal model delta sigma weight residual 108.02 98.90 9.12 1.78e+00 3.16e-01 2.62e+01 ... (remaining 9472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 3662 17.53 - 35.07: 361 35.07 - 52.60: 67 52.60 - 70.14: 10 70.14 - 87.67: 4 Dihedral angle restraints: 4104 sinusoidal: 1569 harmonic: 2535 Sorted by residual: dihedral pdb=" CA GLY A 447 " pdb=" C GLY A 447 " pdb=" N ASN A 448 " pdb=" CA ASN A 448 " ideal model delta harmonic sigma weight residual -180.00 -149.32 -30.68 0 5.00e+00 4.00e-02 3.77e+01 dihedral pdb=" CA GLY B 105 " pdb=" C GLY B 105 " pdb=" N SER B 106 " pdb=" CA SER B 106 " ideal model delta harmonic sigma weight residual 180.00 -154.19 -25.81 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA CYS A 361 " pdb=" C CYS A 361 " pdb=" N VAL A 362 " pdb=" CA VAL A 362 " ideal model delta harmonic sigma weight residual 180.00 157.64 22.36 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 4101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 764 0.058 - 0.116: 204 0.116 - 0.174: 44 0.174 - 0.232: 12 0.232 - 0.290: 2 Chirality restraints: 1026 Sorted by residual: chirality pdb=" CB ILE B 70 " pdb=" CA ILE B 70 " pdb=" CG1 ILE B 70 " pdb=" CG2 ILE B 70 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA TYR E 94 " pdb=" N TYR E 94 " pdb=" C TYR E 94 " pdb=" CB TYR E 94 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CB VAL D 58 " pdb=" CA VAL D 58 " pdb=" CG1 VAL D 58 " pdb=" CG2 VAL D 58 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 1023 not shown) Planarity restraints: 1226 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 58 " 0.046 5.00e-02 4.00e+02 6.92e-02 7.66e+00 pdb=" N PRO D 59 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO D 59 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 59 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 94 " 0.044 5.00e-02 4.00e+02 6.57e-02 6.90e+00 pdb=" N PRO E 95 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO E 95 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 95 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA L 45 " 0.039 5.00e-02 4.00e+02 6.00e-02 5.75e+00 pdb=" N PRO L 46 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO L 46 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO L 46 " 0.033 5.00e-02 4.00e+02 ... (remaining 1223 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1976 2.80 - 3.33: 5469 3.33 - 3.85: 11092 3.85 - 4.38: 12404 4.38 - 4.90: 22385 Nonbonded interactions: 53326 Sorted by model distance: nonbonded pdb=" OG SER H 102 " pdb=" O TYR H 105 " model vdw 2.276 3.040 nonbonded pdb=" O SER L 26 " pdb=" OG SER L 31 " model vdw 2.305 3.040 nonbonded pdb=" OE1 GLN H 6 " pdb=" OG1 THR H 117 " model vdw 2.306 3.040 nonbonded pdb=" O ASP A 442 " pdb=" ND2 ASN A 448 " model vdw 2.321 3.120 nonbonded pdb=" OD1 ASP C 73 " pdb=" OG SER C 75 " model vdw 2.324 3.040 ... (remaining 53321 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 Found NCS groups: ncs_group { reference = (chain 'D' and (resid 1 through 8 or resid 10 through 30 or resid 33 or resid 35 \ through 49 or resid 52 through 54 or resid 56 through 69 or resid 71 through 80 \ or resid 82 through 90 or resid 93 or resid 98 through 103 or resid 105 through \ 107)) selection = (chain 'E' and (resid 1 through 8 or resid 10 through 30 or resid 33 or resid 35 \ through 49 or resid 52 through 54 or resid 56 through 69 or resid 71 through 80 \ or resid 82 through 90 or resid 93 or resid 98 through 103 or resid 105 through \ 107)) } 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=0.50 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: 6.510 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: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.930 Find NCS groups from input model: 0.160 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 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 : 0.007 0.078 6983 Z= 0.320 Angle : 0.938 17.228 9496 Z= 0.536 Chirality : 0.059 0.290 1026 Planarity : 0.007 0.069 1225 Dihedral : 14.214 87.672 2478 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 0.40 % Allowed : 9.69 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -4.20 (0.24), residues: 873 helix: -5.10 (0.18), residues: 24 sheet: -2.74 (0.24), residues: 349 loop : -2.73 (0.23), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 52 HIS 0.006 0.001 HIS B 35 PHE 0.024 0.002 PHE E 83 TYR 0.026 0.002 TYR A 453 ARG 0.007 0.001 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00380 ( 1) link_NAG-ASN : angle 1.90815 ( 3) hydrogen bonds : bond 0.27191 ( 155) hydrogen bonds : angle 10.22394 ( 381) SS BOND : bond 0.00361 ( 8) SS BOND : angle 1.03510 ( 16) covalent geometry : bond 0.00718 ( 6974) covalent geometry : angle 0.93713 ( 9477) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 191 time to evaluate : 0.711 Fit side-chains revert: symmetry clash REVERT: A 495 TYR cc_start: 0.7921 (OUTLIER) cc_final: 0.7602 (m-10) REVERT: B 25 SER cc_start: 0.8764 (t) cc_final: 0.8403 (m) REVERT: C 105 LEU cc_start: 0.8011 (pp) cc_final: 0.7789 (pt) REVERT: D 33 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8201 (tp) REVERT: E 70 GLU cc_start: 0.8315 (pt0) cc_final: 0.8096 (pt0) REVERT: H 62 GLN cc_start: 0.8295 (tm-30) cc_final: 0.8005 (tp40) REVERT: H 74 GLU cc_start: 0.7406 (tm-30) cc_final: 0.7174 (tm-30) REVERT: L 67 SER cc_start: 0.7561 (t) cc_final: 0.7275 (p) outliers start: 3 outliers final: 0 residues processed: 193 average time/residue: 0.2061 time to fit residues: 51.1840 Evaluate side-chains 138 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 136 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain D residue 33 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 0.6980 chunk 65 optimal weight: 0.0770 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 360 ASN A 394 ASN A 506 GLN C 99 HIS D 100 GLN E 38 GLN L 53 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.143332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.115729 restraints weight = 8811.444| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.40 r_work: 0.3212 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3083 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6983 Z= 0.136 Angle : 0.591 11.878 9496 Z= 0.310 Chirality : 0.044 0.182 1026 Planarity : 0.005 0.051 1225 Dihedral : 5.619 46.407 999 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.36 % Allowed : 15.48 % Favored : 81.16 % 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: -3.42 (0.25), residues: 873 helix: -4.95 (0.25), residues: 20 sheet: -2.27 (0.24), residues: 355 loop : -2.14 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 353 HIS 0.003 0.001 HIS C 99 PHE 0.011 0.001 PHE H 64 TYR 0.021 0.001 TYR E 94 ARG 0.005 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00024 ( 1) link_NAG-ASN : angle 1.70236 ( 3) hydrogen bonds : bond 0.03506 ( 155) hydrogen bonds : angle 6.58828 ( 381) SS BOND : bond 0.00281 ( 8) SS BOND : angle 0.83749 ( 16) covalent geometry : bond 0.00314 ( 6974) covalent geometry : angle 0.58939 ( 9477) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.843 Fit side-chains revert: symmetry clash REVERT: A 399 SER cc_start: 0.9282 (t) cc_final: 0.8859 (p) REVERT: A 454 ARG cc_start: 0.7871 (ttm-80) cc_final: 0.7664 (ttm-80) REVERT: A 495 TYR cc_start: 0.8286 (OUTLIER) cc_final: 0.7317 (m-10) REVERT: C 99 HIS cc_start: 0.8634 (OUTLIER) cc_final: 0.7846 (m90) REVERT: D 17 ASP cc_start: 0.8213 (t70) cc_final: 0.8011 (m-30) REVERT: D 33 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7993 (tp) REVERT: H 60 TYR cc_start: 0.8873 (m-10) cc_final: 0.8648 (m-10) REVERT: H 74 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7048 (tm-30) REVERT: H 88 SER cc_start: 0.8558 (t) cc_final: 0.8147 (m) REVERT: H 90 ASP cc_start: 0.8904 (OUTLIER) cc_final: 0.8547 (t0) REVERT: L 67 SER cc_start: 0.7937 (t) cc_final: 0.7688 (p) outliers start: 25 outliers final: 11 residues processed: 147 average time/residue: 0.2398 time to fit residues: 44.8366 Evaluate side-chains 137 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 0.0670 chunk 67 optimal weight: 0.0670 chunk 11 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 3 optimal weight: 6.9990 chunk 48 optimal weight: 0.3980 chunk 49 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN C 99 HIS L 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.140323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.112177 restraints weight = 9018.322| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.42 r_work: 0.3233 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3077 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3077 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6983 Z= 0.116 Angle : 0.558 14.245 9496 Z= 0.289 Chirality : 0.044 0.170 1026 Planarity : 0.004 0.045 1225 Dihedral : 5.096 33.506 999 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.96 % Allowed : 18.03 % Favored : 79.00 % 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: -2.93 (0.26), residues: 873 helix: -4.64 (0.41), residues: 20 sheet: -1.96 (0.25), residues: 349 loop : -1.79 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 36 HIS 0.010 0.002 HIS C 99 PHE 0.010 0.001 PHE A 377 TYR 0.019 0.001 TYR E 94 ARG 0.003 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00032 ( 1) link_NAG-ASN : angle 1.43763 ( 3) hydrogen bonds : bond 0.02970 ( 155) hydrogen bonds : angle 5.77292 ( 381) SS BOND : bond 0.00235 ( 8) SS BOND : angle 0.56861 ( 16) covalent geometry : bond 0.00268 ( 6974) covalent geometry : angle 0.55775 ( 9477) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: A 399 SER cc_start: 0.9250 (t) cc_final: 0.8819 (p) REVERT: A 449 TYR cc_start: 0.8731 (p90) cc_final: 0.8421 (p90) REVERT: C 99 HIS cc_start: 0.8763 (OUTLIER) cc_final: 0.7704 (m170) REVERT: D 33 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8041 (tp) REVERT: H 74 GLU cc_start: 0.7810 (tm-30) cc_final: 0.6962 (tm-30) REVERT: H 88 SER cc_start: 0.8594 (t) cc_final: 0.8182 (m) REVERT: H 90 ASP cc_start: 0.8901 (OUTLIER) cc_final: 0.8587 (t0) REVERT: L 74 SER cc_start: 0.8220 (p) cc_final: 0.7979 (t) outliers start: 22 outliers final: 12 residues processed: 141 average time/residue: 0.2140 time to fit residues: 39.0443 Evaluate side-chains 129 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN C 99 HIS H 39 GLN L 40 GLN L 53 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.135767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.107054 restraints weight = 9122.873| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.44 r_work: 0.3118 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2977 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 6983 Z= 0.224 Angle : 0.634 14.110 9496 Z= 0.329 Chirality : 0.046 0.211 1026 Planarity : 0.004 0.044 1225 Dihedral : 5.126 32.445 997 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 4.31 % Allowed : 19.11 % Favored : 76.58 % 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: -2.80 (0.27), residues: 873 helix: -4.66 (0.44), residues: 20 sheet: -1.95 (0.25), residues: 358 loop : -1.60 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 47 HIS 0.008 0.002 HIS C 99 PHE 0.014 0.002 PHE A 377 TYR 0.020 0.002 TYR E 94 ARG 0.003 0.001 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00248 ( 1) link_NAG-ASN : angle 1.41254 ( 3) hydrogen bonds : bond 0.02963 ( 155) hydrogen bonds : angle 5.71494 ( 381) SS BOND : bond 0.00233 ( 8) SS BOND : angle 0.78613 ( 16) covalent geometry : bond 0.00531 ( 6974) covalent geometry : angle 0.63335 ( 9477) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: A 399 SER cc_start: 0.9228 (t) cc_final: 0.8795 (p) REVERT: A 449 TYR cc_start: 0.8865 (p90) cc_final: 0.8574 (p90) REVERT: A 483 VAL cc_start: 0.8766 (t) cc_final: 0.8520 (p) REVERT: B 13 GLN cc_start: 0.8660 (mm-40) cc_final: 0.8237 (mt0) REVERT: C 34 MET cc_start: 0.6729 (ptp) cc_final: 0.6298 (mtp) REVERT: C 99 HIS cc_start: 0.8821 (OUTLIER) cc_final: 0.7840 (m170) REVERT: H 74 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7096 (tm-30) REVERT: H 88 SER cc_start: 0.8825 (t) cc_final: 0.8387 (m) REVERT: H 90 ASP cc_start: 0.8939 (OUTLIER) cc_final: 0.8476 (t0) REVERT: L 74 SER cc_start: 0.8598 (p) cc_final: 0.8289 (t) outliers start: 32 outliers final: 20 residues processed: 147 average time/residue: 0.2243 time to fit residues: 42.3266 Evaluate side-chains 140 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 13 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 2 optimal weight: 0.0980 chunk 12 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 67 optimal weight: 0.0570 chunk 66 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN C 99 HIS L 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.137969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.109204 restraints weight = 9013.002| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.46 r_work: 0.3148 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3027 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3027 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6983 Z= 0.115 Angle : 0.570 14.161 9496 Z= 0.291 Chirality : 0.044 0.208 1026 Planarity : 0.004 0.041 1225 Dihedral : 4.616 22.515 995 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.77 % Allowed : 20.05 % Favored : 76.18 % 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: -2.49 (0.27), residues: 873 helix: -4.60 (0.47), residues: 20 sheet: -1.82 (0.26), residues: 352 loop : -1.33 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 36 HIS 0.005 0.001 HIS C 99 PHE 0.017 0.001 PHE D 71 TYR 0.020 0.001 TYR E 94 ARG 0.003 0.000 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00013 ( 1) link_NAG-ASN : angle 1.13460 ( 3) hydrogen bonds : bond 0.02599 ( 155) hydrogen bonds : angle 5.35032 ( 381) SS BOND : bond 0.00260 ( 8) SS BOND : angle 0.56702 ( 16) covalent geometry : bond 0.00267 ( 6974) covalent geometry : angle 0.56927 ( 9477) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 124 time to evaluate : 0.819 Fit side-chains revert: symmetry clash REVERT: A 399 SER cc_start: 0.9226 (t) cc_final: 0.8790 (p) REVERT: A 449 TYR cc_start: 0.8785 (p90) cc_final: 0.8560 (p90) REVERT: A 483 VAL cc_start: 0.8644 (t) cc_final: 0.8405 (p) REVERT: B 13 GLN cc_start: 0.8610 (mm-40) cc_final: 0.8214 (mt0) REVERT: H 10 GLU cc_start: 0.8464 (mp0) cc_final: 0.8263 (mp0) REVERT: H 62 GLN cc_start: 0.8481 (tm-30) cc_final: 0.7939 (tp-100) REVERT: H 74 GLU cc_start: 0.7788 (tm-30) cc_final: 0.6981 (tm-30) REVERT: H 88 SER cc_start: 0.8805 (t) cc_final: 0.8356 (m) REVERT: L 74 SER cc_start: 0.8543 (p) cc_final: 0.8245 (t) outliers start: 28 outliers final: 19 residues processed: 144 average time/residue: 0.2085 time to fit residues: 39.7199 Evaluate side-chains 137 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 74 optimal weight: 2.9990 chunk 31 optimal weight: 0.0980 chunk 40 optimal weight: 0.7980 chunk 79 optimal weight: 0.0470 chunk 48 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN C 99 HIS ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.138415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.109580 restraints weight = 8997.580| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.48 r_work: 0.3188 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6983 Z= 0.113 Angle : 0.555 14.189 9496 Z= 0.283 Chirality : 0.044 0.171 1026 Planarity : 0.004 0.041 1225 Dihedral : 4.441 21.132 995 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.50 % Allowed : 20.59 % Favored : 75.91 % 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: -2.29 (0.28), residues: 873 helix: -4.56 (0.48), residues: 20 sheet: -1.69 (0.26), residues: 352 loop : -1.18 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 36 HIS 0.003 0.001 HIS C 99 PHE 0.016 0.001 PHE A 377 TYR 0.022 0.001 TYR B 60 ARG 0.003 0.000 ARG H 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00012 ( 1) link_NAG-ASN : angle 1.13115 ( 3) hydrogen bonds : bond 0.02467 ( 155) hydrogen bonds : angle 5.14458 ( 381) SS BOND : bond 0.00240 ( 8) SS BOND : angle 0.52140 ( 16) covalent geometry : bond 0.00264 ( 6974) covalent geometry : angle 0.55528 ( 9477) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.712 Fit side-chains revert: symmetry clash REVERT: A 399 SER cc_start: 0.9197 (t) cc_final: 0.8783 (p) REVERT: A 483 VAL cc_start: 0.8604 (t) cc_final: 0.8355 (p) REVERT: B 13 GLN cc_start: 0.8632 (mm-40) cc_final: 0.8230 (mt0) REVERT: C 34 MET cc_start: 0.6463 (ptp) cc_final: 0.6156 (mtm) REVERT: H 62 GLN cc_start: 0.8449 (tm-30) cc_final: 0.7911 (tp-100) REVERT: H 74 GLU cc_start: 0.7787 (tm-30) cc_final: 0.6946 (tm-30) REVERT: H 88 SER cc_start: 0.8777 (t) cc_final: 0.8339 (m) REVERT: H 90 ASP cc_start: 0.8867 (OUTLIER) cc_final: 0.8380 (t0) REVERT: L 74 SER cc_start: 0.8494 (p) cc_final: 0.8211 (t) outliers start: 26 outliers final: 20 residues processed: 147 average time/residue: 0.2141 time to fit residues: 40.7443 Evaluate side-chains 144 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 64 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 21 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN C 99 HIS ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.137822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.109169 restraints weight = 9031.315| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.47 r_work: 0.3163 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3021 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3021 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6983 Z= 0.151 Angle : 0.572 13.769 9496 Z= 0.294 Chirality : 0.045 0.186 1026 Planarity : 0.004 0.041 1225 Dihedral : 4.535 22.935 995 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.63 % Allowed : 20.59 % Favored : 75.77 % 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: -2.25 (0.28), residues: 873 helix: -4.52 (0.54), residues: 20 sheet: -1.68 (0.26), residues: 352 loop : -1.13 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 47 HIS 0.006 0.001 HIS C 99 PHE 0.022 0.001 PHE A 377 TYR 0.018 0.001 TYR E 94 ARG 0.004 0.000 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00071 ( 1) link_NAG-ASN : angle 1.17083 ( 3) hydrogen bonds : bond 0.02503 ( 155) hydrogen bonds : angle 5.17757 ( 381) SS BOND : bond 0.00220 ( 8) SS BOND : angle 0.60526 ( 16) covalent geometry : bond 0.00360 ( 6974) covalent geometry : angle 0.57135 ( 9477) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 399 SER cc_start: 0.9229 (t) cc_final: 0.8777 (p) REVERT: A 483 VAL cc_start: 0.8664 (t) cc_final: 0.8435 (p) REVERT: B 13 GLN cc_start: 0.8653 (mm-40) cc_final: 0.8248 (mt0) REVERT: H 62 GLN cc_start: 0.8513 (tm-30) cc_final: 0.7978 (tp-100) REVERT: H 74 GLU cc_start: 0.7793 (tm-30) cc_final: 0.6973 (tm-30) REVERT: H 87 ARG cc_start: 0.7392 (ttp-110) cc_final: 0.7161 (ttp80) REVERT: H 88 SER cc_start: 0.8803 (t) cc_final: 0.8357 (m) REVERT: L 74 SER cc_start: 0.8565 (p) cc_final: 0.8305 (t) outliers start: 27 outliers final: 22 residues processed: 143 average time/residue: 0.2788 time to fit residues: 52.6572 Evaluate side-chains 144 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 33 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 80 optimal weight: 0.0670 chunk 32 optimal weight: 9.9990 overall best weight: 1.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN B 84 ASN C 99 HIS D 79 GLN ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.134690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.105895 restraints weight = 9173.016| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.48 r_work: 0.3089 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 6983 Z= 0.237 Angle : 0.635 13.707 9496 Z= 0.330 Chirality : 0.046 0.213 1026 Planarity : 0.004 0.052 1225 Dihedral : 4.919 26.346 995 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 4.04 % Allowed : 20.19 % Favored : 75.77 % 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: -2.31 (0.28), residues: 873 helix: -4.57 (0.52), residues: 20 sheet: -1.73 (0.26), residues: 354 loop : -1.17 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 47 HIS 0.017 0.003 HIS C 99 PHE 0.025 0.002 PHE A 377 TYR 0.024 0.002 TYR A 453 ARG 0.005 0.001 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00243 ( 1) link_NAG-ASN : angle 1.35811 ( 3) hydrogen bonds : bond 0.02760 ( 155) hydrogen bonds : angle 5.45187 ( 381) SS BOND : bond 0.00249 ( 8) SS BOND : angle 0.75929 ( 16) covalent geometry : bond 0.00569 ( 6974) covalent geometry : angle 0.63446 ( 9477) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.666 Fit side-chains revert: symmetry clash REVERT: A 399 SER cc_start: 0.9292 (t) cc_final: 0.8833 (p) REVERT: A 403 ARG cc_start: 0.7014 (ptp-170) cc_final: 0.6067 (ptm160) REVERT: A 483 VAL cc_start: 0.8784 (t) cc_final: 0.8563 (p) REVERT: H 62 GLN cc_start: 0.8610 (tm-30) cc_final: 0.8077 (tp-100) REVERT: H 74 GLU cc_start: 0.7771 (tm-30) cc_final: 0.6950 (tm-30) REVERT: H 88 SER cc_start: 0.8920 (t) cc_final: 0.8398 (m) REVERT: H 90 ASP cc_start: 0.8769 (t0) cc_final: 0.8177 (t0) REVERT: L 74 SER cc_start: 0.8730 (p) cc_final: 0.8437 (t) outliers start: 30 outliers final: 24 residues processed: 147 average time/residue: 0.2019 time to fit residues: 38.9129 Evaluate side-chains 147 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 17 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 3 optimal weight: 0.3980 chunk 78 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN C 99 HIS ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.132388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.102861 restraints weight = 9236.262| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.57 r_work: 0.3062 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 6983 Z= 0.224 Angle : 0.630 13.563 9496 Z= 0.328 Chirality : 0.047 0.216 1026 Planarity : 0.004 0.049 1225 Dihedral : 4.961 27.753 995 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 4.17 % Allowed : 20.46 % Favored : 75.37 % 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: -2.29 (0.28), residues: 873 helix: -4.54 (0.56), residues: 20 sheet: -1.65 (0.26), residues: 346 loop : -1.23 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 47 HIS 0.005 0.002 HIS C 99 PHE 0.030 0.002 PHE A 377 TYR 0.021 0.002 TYR A 453 ARG 0.004 0.001 ARG B 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00223 ( 1) link_NAG-ASN : angle 1.34419 ( 3) hydrogen bonds : bond 0.02736 ( 155) hydrogen bonds : angle 5.49060 ( 381) SS BOND : bond 0.00216 ( 8) SS BOND : angle 0.68574 ( 16) covalent geometry : bond 0.00536 ( 6974) covalent geometry : angle 0.62993 ( 9477) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 0.689 Fit side-chains revert: symmetry clash REVERT: A 399 SER cc_start: 0.9300 (t) cc_final: 0.8839 (p) REVERT: A 403 ARG cc_start: 0.6968 (ptp-170) cc_final: 0.5967 (ptm160) REVERT: A 483 VAL cc_start: 0.8791 (t) cc_final: 0.8589 (p) REVERT: B 16 ARG cc_start: 0.8324 (tpp80) cc_final: 0.7750 (ttm170) REVERT: H 62 GLN cc_start: 0.8559 (tm-30) cc_final: 0.8005 (tp-100) REVERT: H 74 GLU cc_start: 0.7639 (tm-30) cc_final: 0.6784 (tm-30) REVERT: H 88 SER cc_start: 0.8932 (t) cc_final: 0.8430 (m) REVERT: H 90 ASP cc_start: 0.8680 (t0) cc_final: 0.8037 (t0) REVERT: L 74 SER cc_start: 0.8683 (p) cc_final: 0.8376 (t) REVERT: L 81 GLN cc_start: 0.7716 (pm20) cc_final: 0.7431 (mp10) outliers start: 31 outliers final: 26 residues processed: 155 average time/residue: 0.2633 time to fit residues: 52.2049 Evaluate side-chains 153 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 32 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 74 optimal weight: 0.2980 chunk 24 optimal weight: 0.0470 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN C 82 GLN C 99 HIS ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.138088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.109063 restraints weight = 9178.830| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.58 r_work: 0.3122 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2973 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6983 Z= 0.131 Angle : 0.587 13.898 9496 Z= 0.302 Chirality : 0.045 0.181 1026 Planarity : 0.004 0.041 1225 Dihedral : 4.713 25.867 995 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.23 % Allowed : 22.07 % Favored : 74.70 % 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: -2.15 (0.28), residues: 873 helix: -4.51 (0.54), residues: 20 sheet: -1.51 (0.26), residues: 348 loop : -1.16 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 47 HIS 0.008 0.002 HIS C 99 PHE 0.036 0.002 PHE A 377 TYR 0.020 0.001 TYR E 94 ARG 0.003 0.000 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00037 ( 1) link_NAG-ASN : angle 1.19190 ( 3) hydrogen bonds : bond 0.02626 ( 155) hydrogen bonds : angle 5.35451 ( 381) SS BOND : bond 0.00212 ( 8) SS BOND : angle 1.48065 ( 16) covalent geometry : bond 0.00312 ( 6974) covalent geometry : angle 0.58374 ( 9477) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.777 Fit side-chains revert: symmetry clash REVERT: A 399 SER cc_start: 0.9260 (t) cc_final: 0.8798 (p) REVERT: A 403 ARG cc_start: 0.6909 (ptp-170) cc_final: 0.5925 (ptm160) REVERT: A 483 VAL cc_start: 0.8495 (t) cc_final: 0.8240 (p) REVERT: B 16 ARG cc_start: 0.8355 (tpp80) cc_final: 0.7762 (ttm170) REVERT: H 62 GLN cc_start: 0.8543 (tm-30) cc_final: 0.8014 (tp-100) REVERT: H 88 SER cc_start: 0.8870 (t) cc_final: 0.8320 (m) REVERT: H 90 ASP cc_start: 0.8766 (t0) cc_final: 0.8141 (t0) REVERT: L 74 SER cc_start: 0.8670 (p) cc_final: 0.8376 (t) REVERT: L 81 GLN cc_start: 0.7649 (pm20) cc_final: 0.7390 (mp10) outliers start: 24 outliers final: 22 residues processed: 145 average time/residue: 0.2104 time to fit residues: 39.7014 Evaluate side-chains 147 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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: 67.9653 > 50: distance: 35 - 277: 32.335 distance: 38 - 274: 32.711 distance: 48 - 263: 33.069 distance: 51 - 260: 32.679 distance: 65 - 240: 32.223 distance: 68 - 237: 25.368 distance: 116 - 270: 33.157 distance: 119 - 267: 23.256 distance: 128 - 252: 32.882 distance: 131 - 249: 36.124 distance: 196 - 198: 35.299 distance: 198 - 199: 32.789 distance: 199 - 200: 36.056 distance: 199 - 202: 26.885 distance: 200 - 201: 32.843 distance: 200 - 205: 33.216 distance: 202 - 203: 60.279 distance: 202 - 204: 50.804 distance: 205 - 206: 9.581 distance: 206 - 207: 29.711 distance: 207 - 208: 39.138 distance: 207 - 209: 40.543 distance: 209 - 210: 58.231 distance: 210 - 211: 48.700 distance: 210 - 213: 27.850 distance: 211 - 212: 56.022 distance: 211 - 221: 8.261 distance: 213 - 214: 7.876 distance: 214 - 215: 30.418 distance: 214 - 216: 25.147 distance: 215 - 217: 22.659 distance: 216 - 218: 17.297 distance: 217 - 219: 10.225 distance: 218 - 219: 9.753 distance: 219 - 220: 26.947 distance: 221 - 222: 24.138 distance: 222 - 223: 38.760 distance: 222 - 225: 30.737 distance: 223 - 224: 31.151 distance: 223 - 230: 33.366 distance: 225 - 226: 25.684 distance: 226 - 227: 17.466 distance: 227 - 228: 23.399 distance: 227 - 229: 42.796 distance: 230 - 231: 19.297 distance: 230 - 236: 36.969 distance: 231 - 232: 42.419 distance: 231 - 234: 31.792 distance: 232 - 233: 34.016 distance: 232 - 237: 43.248 distance: 234 - 235: 9.458 distance: 235 - 236: 40.220 distance: 237 - 238: 38.918 distance: 238 - 239: 3.588 distance: 238 - 241: 43.248 distance: 239 - 240: 32.963 distance: 239 - 249: 56.859 distance: 241 - 242: 35.893 distance: 242 - 243: 30.700 distance: 242 - 244: 23.072 distance: 243 - 245: 23.755 distance: 244 - 246: 32.764 distance: 245 - 247: 14.514 distance: 246 - 247: 12.936 distance: 247 - 248: 13.535 distance: 250 - 251: 24.073 distance: 250 - 253: 64.427 distance: 251 - 252: 8.460 distance: 251 - 260: 50.102 distance: 253 - 254: 37.377 distance: 254 - 255: 13.623 distance: 255 - 256: 11.109 distance: 256 - 257: 38.874 distance: 257 - 258: 31.749 distance: 257 - 259: 20.368 distance: 260 - 261: 23.076 distance: 261 - 262: 15.424 distance: 261 - 264: 49.257 distance: 262 - 263: 40.999 distance: 262 - 267: 45.837 distance: 264 - 265: 25.684 distance: 264 - 266: 23.324 distance: 267 - 268: 33.213 distance: 268 - 269: 29.288 distance: 268 - 271: 53.710 distance: 269 - 270: 5.722 distance: 269 - 274: 50.873 distance: 271 - 272: 38.783 distance: 271 - 273: 36.076 distance: 274 - 275: 27.509 distance: 275 - 276: 3.750 distance: 275 - 278: 15.572 distance: 276 - 277: 9.177 distance: 276 - 281: 34.769 distance: 278 - 279: 33.768 distance: 278 - 280: 22.209