Starting phenix.real_space_refine on Thu Mar 6 05:02:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cb3_45413/03_2025/9cb3_45413.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cb3_45413/03_2025/9cb3_45413.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cb3_45413/03_2025/9cb3_45413.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cb3_45413/03_2025/9cb3_45413.map" model { file = "/net/cci-nas-00/data/ceres_data/9cb3_45413/03_2025/9cb3_45413.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cb3_45413/03_2025/9cb3_45413.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 3183 2.51 5 N 882 2.21 5 O 902 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4995 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 3912 Classifications: {'peptide': 519} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 504} Unresolved non-hydrogen bonds: 223 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 153 Chain: "B" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 967 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 7, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 90 Chain: "C" Number of atoms: 116 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 10} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 10} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 94 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG C 85 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 85 " occ=0.50 Time building chain proxies: 3.42, per 1000 atoms: 0.68 Number of scatterers: 4995 At special positions: 0 Unit cell: (77.655, 83.5, 97.695, 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 28 16.00 O 902 8.00 N 882 7.00 C 3183 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 603.8 milliseconds 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1296 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 0 sheets defined 72.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 31 through 35 removed outlier: 3.617A pdb=" N LEU A 35 " --> pdb=" O ILE A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 44 Processing helix chain 'A' and resid 45 through 47 No H-bonds generated for 'chain 'A' and resid 45 through 47' Processing helix chain 'A' and resid 48 through 56 Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 70 through 75 Processing helix chain 'A' and resid 84 through 86 No H-bonds generated for 'chain 'A' and resid 84 through 86' Processing helix chain 'A' and resid 87 through 97 removed outlier: 3.684A pdb=" N PHE A 91 " --> pdb=" O ASN A 87 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 113 removed outlier: 3.929A pdb=" N ALA A 103 " --> pdb=" O ASN A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 141 removed outlier: 3.988A pdb=" N VAL A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 153 removed outlier: 3.671A pdb=" N PHE A 152 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE A 153 " --> pdb=" O TRP A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 179 Processing helix chain 'A' and resid 183 through 196 removed outlier: 4.088A pdb=" N LEU A 196 " --> pdb=" O ARG A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 217 removed outlier: 3.510A pdb=" N GLU A 212 " --> pdb=" O ASP A 208 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN A 216 " --> pdb=" O GLU A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 231 removed outlier: 3.725A pdb=" N ARG A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 254 removed outlier: 3.668A pdb=" N LYS A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY A 254 " --> pdb=" O TYR A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 266 removed outlier: 3.647A pdb=" N LYS A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 288 Processing helix chain 'A' and resid 296 through 302 removed outlier: 3.644A pdb=" N GLN A 302 " --> pdb=" O VAL A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 324 Processing helix chain 'A' and resid 327 through 345 Processing helix chain 'A' and resid 348 through 350 No H-bonds generated for 'chain 'A' and resid 348 through 350' Processing helix chain 'A' and resid 351 through 367 Processing helix chain 'A' and resid 373 through 380 removed outlier: 3.545A pdb=" N TRP A 379 " --> pdb=" O ARG A 375 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 380 " --> pdb=" O GLU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 401 Processing helix chain 'A' and resid 409 through 419 removed outlier: 3.851A pdb=" N TYR A 413 " --> pdb=" O THR A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 437 Processing helix chain 'A' and resid 442 through 447 removed outlier: 3.630A pdb=" N TYR A 447 " --> pdb=" O LEU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 464 removed outlier: 3.612A pdb=" N HIS A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 479 Processing helix chain 'A' and resid 485 through 498 Processing helix chain 'A' and resid 511 through 517 Processing helix chain 'A' and resid 518 through 523 removed outlier: 6.235A pdb=" N ARG A 521 " --> pdb=" O GLU A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 528 removed outlier: 3.789A pdb=" N GLN A 527 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 541 Processing helix chain 'B' and resid 17 through 22 Processing helix chain 'B' and resid 24 through 35 removed outlier: 3.954A pdb=" N LYS B 28 " --> pdb=" O SER B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 65 Processing helix chain 'B' and resid 86 through 93 Processing helix chain 'B' and resid 96 through 111 Processing helix chain 'B' and resid 116 through 129 removed outlier: 3.778A pdb=" N MET B 126 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY B 129 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 139 Processing helix chain 'B' and resid 146 through 148 No H-bonds generated for 'chain 'B' and resid 146 through 148' Processing helix chain 'B' and resid 149 through 157 293 hydrogen bonds defined for protein. 858 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: 1.23 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.41: 2036 1.41 - 1.64: 3012 1.64 - 1.87: 36 1.87 - 2.10: 0 2.10 - 2.33: 1 Bond restraints: 5085 Sorted by residual: bond pdb=" C GLY C 84 " pdb=" N AARG C 85 " ideal model delta sigma weight residual 1.331 2.335 -1.004 2.07e-02 2.33e+03 2.35e+03 bond pdb=" C GLY C 84 " pdb=" N BARG C 85 " ideal model delta sigma weight residual 1.331 1.175 0.156 2.07e-02 2.33e+03 5.67e+01 bond pdb=" C SER A 77 " pdb=" O SER A 77 " ideal model delta sigma weight residual 1.234 1.180 0.054 1.35e-02 5.49e+03 1.61e+01 bond pdb=" CA ALA A 76 " pdb=" CB ALA A 76 " ideal model delta sigma weight residual 1.530 1.471 0.059 1.58e-02 4.01e+03 1.39e+01 bond pdb=" C SER A 77 " pdb=" N PHE A 78 " ideal model delta sigma weight residual 1.329 1.287 0.042 1.23e-02 6.61e+03 1.17e+01 ... (remaining 5080 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.23: 6918 14.23 - 28.45: 1 28.45 - 42.68: 4 42.68 - 56.90: 1 56.90 - 71.13: 1 Bond angle restraints: 6925 Sorted by residual: angle pdb=" O GLY C 84 " pdb=" C GLY C 84 " pdb=" N AARG C 85 " ideal model delta sigma weight residual 123.00 72.01 50.99 1.60e+00 3.91e-01 1.02e+03 angle pdb=" C GLY C 84 " pdb=" N AARG C 85 " pdb=" CA AARG C 85 " ideal model delta sigma weight residual 121.80 50.67 71.13 2.44e+00 1.68e-01 8.50e+02 angle pdb=" O GLY C 84 " pdb=" C GLY C 84 " pdb=" N BARG C 85 " ideal model delta sigma weight residual 123.00 162.27 -39.27 1.60e+00 3.91e-01 6.02e+02 angle pdb=" CA GLY C 84 " pdb=" C GLY C 84 " pdb=" N BARG C 85 " ideal model delta sigma weight residual 116.20 78.13 38.07 2.00e+00 2.50e-01 3.62e+02 angle pdb=" CA GLY C 84 " pdb=" C GLY C 84 " pdb=" N AARG C 85 " ideal model delta sigma weight residual 116.20 153.14 -36.94 2.00e+00 2.50e-01 3.41e+02 ... (remaining 6920 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 2927 35.98 - 71.97: 117 71.97 - 107.95: 6 107.95 - 143.93: 1 143.93 - 179.91: 1 Dihedral angle restraints: 3052 sinusoidal: 1073 harmonic: 1979 Sorted by residual: dihedral pdb=" CA GLY C 84 " pdb=" C GLY C 84 " pdb=" N AARG C 85 " pdb=" CA AARG C 85 " ideal model delta harmonic sigma weight residual 180.00 71.66 108.34 0 5.00e+00 4.00e-02 4.70e+02 dihedral pdb=" CD BARG C 85 " pdb=" NE BARG C 85 " pdb=" CZ BARG C 85 " pdb=" NH1BARG C 85 " ideal model delta sinusoidal sigma weight residual 0.00 179.91 -179.91 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" C ASN B 108 " pdb=" N ASN B 108 " pdb=" CA ASN B 108 " pdb=" CB ASN B 108 " ideal model delta harmonic sigma weight residual -122.60 -110.00 -12.60 0 2.50e+00 1.60e-01 2.54e+01 ... (remaining 3049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 758 0.068 - 0.136: 61 0.136 - 0.205: 6 0.205 - 0.273: 4 0.273 - 0.341: 1 Chirality restraints: 830 Sorted by residual: chirality pdb=" CA ASN B 108 " pdb=" N ASN B 108 " pdb=" C ASN B 108 " pdb=" CB ASN B 108 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CA ILE B 112 " pdb=" N ILE B 112 " pdb=" C ILE B 112 " pdb=" CB ILE B 112 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CG LEU A 434 " pdb=" CB LEU A 434 " pdb=" CD1 LEU A 434 " pdb=" CD2 LEU A 434 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 827 not shown) Planarity restraints: 879 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 84 " -0.127 2.00e-02 2.50e+03 1.43e-01 2.05e+02 pdb=" C GLY C 84 " 0.242 2.00e-02 2.50e+03 pdb=" O GLY C 84 " -0.044 2.00e-02 2.50e+03 pdb=" N AARG C 85 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 102 " 0.025 2.00e-02 2.50e+03 4.93e-02 2.43e+01 pdb=" C GLU B 102 " -0.085 2.00e-02 2.50e+03 pdb=" O GLU B 102 " 0.032 2.00e-02 2.50e+03 pdb=" N LEU B 103 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 84 " -0.006 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C GLY C 84 " 0.063 2.00e-02 2.50e+03 pdb=" O GLY C 84 " -0.029 2.00e-02 2.50e+03 pdb=" N BARG C 85 " -0.028 2.00e-02 2.50e+03 ... (remaining 876 not shown) Histogram of nonbonded interaction distances: 1.29 - 2.01: 2 2.01 - 2.74: 414 2.74 - 3.46: 7399 3.46 - 4.18: 10668 4.18 - 4.90: 19337 Nonbonded interactions: 37820 Sorted by model distance: nonbonded pdb=" C GLY C 84 " pdb=" CB AARG C 85 " model vdw 1.293 2.936 nonbonded pdb=" N GLY C 84 " pdb=" N BARG C 85 " model vdw 1.931 2.560 nonbonded pdb=" O GLY C 84 " pdb=" CB AARG C 85 " model vdw 2.196 3.440 nonbonded pdb=" OG SER A 158 " pdb=" O SER A 160 " model vdw 2.202 3.040 nonbonded pdb=" O TYR A 350 " pdb=" OH TYR A 385 " model vdw 2.244 3.040 ... (remaining 37815 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.010 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.440 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6519 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 : 0.015 1.004 5085 Z= 0.539 Angle : 1.615 71.125 6925 Z= 0.857 Chirality : 0.046 0.341 830 Planarity : 0.007 0.143 879 Dihedral : 18.757 179.913 1756 Min Nonbonded Distance : 1.293 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.46 % Allowed : 33.33 % Favored : 65.21 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.34), residues: 661 helix: 0.65 (0.26), residues: 451 sheet: None (None), residues: 0 loop : -1.27 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 73 HIS 0.004 0.001 HIS A 69 PHE 0.025 0.002 PHE A 210 TYR 0.017 0.002 TYR A 223 ARG 0.004 0.000 ARG A 461 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.559 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 81 average time/residue: 0.1700 time to fit residues: 18.1289 Evaluate side-chains 75 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain B residue 153 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 26 optimal weight: 0.0470 chunk 51 optimal weight: 9.9990 chunk 20 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 38 optimal weight: 0.0770 chunk 59 optimal weight: 4.9990 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.222458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.173039 restraints weight = 6850.506| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 3.55 r_work: 0.3816 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3822 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3822 r_free = 0.3822 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3821 r_free = 0.3821 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5085 Z= 0.175 Angle : 0.626 13.566 6925 Z= 0.320 Chirality : 0.039 0.277 830 Planarity : 0.005 0.055 879 Dihedral : 8.306 178.821 719 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.09 % Favored : 95.76 % Rotamer: Outliers : 5.21 % Allowed : 29.17 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.34), residues: 662 helix: 1.02 (0.25), residues: 457 sheet: None (None), residues: 0 loop : -1.12 (0.45), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 82 HIS 0.003 0.001 HIS A 69 PHE 0.014 0.001 PHE B 101 TYR 0.018 0.002 TYR A 341 ARG 0.002 0.000 ARG A 521 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 SER cc_start: 0.8056 (t) cc_final: 0.7557 (t) REVERT: A 452 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7252 (tt) REVERT: A 486 ILE cc_start: 0.6566 (OUTLIER) cc_final: 0.6246 (mp) outliers start: 24 outliers final: 12 residues processed: 102 average time/residue: 0.1748 time to fit residues: 23.9539 Evaluate side-chains 86 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 153 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 12 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 20 optimal weight: 0.3980 chunk 1 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.222790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.162478 restraints weight = 6294.042| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 3.72 r_work: 0.3779 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3783 r_free = 0.3783 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3783 r_free = 0.3783 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5085 Z= 0.185 Angle : 0.588 10.677 6925 Z= 0.293 Chirality : 0.040 0.261 830 Planarity : 0.005 0.047 879 Dihedral : 8.079 179.036 718 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 5.62 % Allowed : 28.54 % Favored : 65.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.34), residues: 662 helix: 1.25 (0.26), residues: 452 sheet: None (None), residues: 0 loop : -0.96 (0.45), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 73 HIS 0.003 0.001 HIS A 69 PHE 0.012 0.001 PHE A 497 TYR 0.024 0.002 TYR A 341 ARG 0.006 0.000 ARG A 461 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LEU cc_start: 0.7228 (tp) cc_final: 0.6815 (mt) REVERT: A 452 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7211 (tt) REVERT: A 486 ILE cc_start: 0.6485 (OUTLIER) cc_final: 0.6164 (mp) REVERT: A 519 ASP cc_start: 0.8579 (t70) cc_final: 0.8098 (t0) outliers start: 26 outliers final: 19 residues processed: 97 average time/residue: 0.1605 time to fit residues: 20.3619 Evaluate side-chains 93 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 521 ARG Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 153 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 40 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 65 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.219150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.151370 restraints weight = 13121.777| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 5.62 r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3821 r_free = 0.3821 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3821 r_free = 0.3821 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5085 Z= 0.230 Angle : 0.589 12.325 6925 Z= 0.295 Chirality : 0.039 0.196 830 Planarity : 0.005 0.045 879 Dihedral : 8.033 179.716 718 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 6.46 % Allowed : 28.54 % Favored : 65.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.34), residues: 662 helix: 1.23 (0.26), residues: 454 sheet: None (None), residues: 0 loop : -1.01 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 73 HIS 0.002 0.001 HIS A 69 PHE 0.015 0.002 PHE A 433 TYR 0.028 0.003 TYR A 341 ARG 0.006 0.000 ARG A 461 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 79 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: A 101 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6477 (tt0) REVERT: A 129 LEU cc_start: 0.7233 (tp) cc_final: 0.6807 (mt) REVERT: A 204 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7928 (pp30) REVERT: A 452 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7261 (tt) REVERT: A 486 ILE cc_start: 0.6783 (OUTLIER) cc_final: 0.6474 (mp) outliers start: 30 outliers final: 19 residues processed: 97 average time/residue: 0.1615 time to fit residues: 20.9345 Evaluate side-chains 99 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 521 ARG Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 153 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 1 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 49 optimal weight: 0.0470 chunk 48 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.218860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.163328 restraints weight = 6246.407| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 3.92 r_work: 0.3803 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3802 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3802 r_free = 0.3802 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3802 r_free = 0.3802 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3802 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5085 Z= 0.164 Angle : 0.565 12.005 6925 Z= 0.277 Chirality : 0.038 0.179 830 Planarity : 0.004 0.047 879 Dihedral : 7.880 179.112 718 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 5.83 % Allowed : 30.21 % Favored : 63.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.35), residues: 662 helix: 1.36 (0.26), residues: 457 sheet: None (None), residues: 0 loop : -0.91 (0.46), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 73 HIS 0.002 0.001 HIS A 169 PHE 0.014 0.001 PHE A 497 TYR 0.026 0.002 TYR A 341 ARG 0.005 0.000 ARG A 461 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 81 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LEU cc_start: 0.7303 (tp) cc_final: 0.6899 (mt) REVERT: A 255 CYS cc_start: 0.6621 (OUTLIER) cc_final: 0.6346 (t) REVERT: A 287 PHE cc_start: 0.6618 (OUTLIER) cc_final: 0.5761 (t80) REVERT: A 452 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7198 (tt) REVERT: A 486 ILE cc_start: 0.6556 (OUTLIER) cc_final: 0.6256 (mp) REVERT: A 519 ASP cc_start: 0.8605 (t70) cc_final: 0.8092 (t0) REVERT: A 521 ARG cc_start: 0.7281 (OUTLIER) cc_final: 0.7056 (tmm160) REVERT: A 524 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7849 (mt-10) REVERT: B 156 GLU cc_start: 0.3981 (mm-30) cc_final: 0.3779 (pt0) outliers start: 27 outliers final: 17 residues processed: 99 average time/residue: 0.1712 time to fit residues: 22.4399 Evaluate side-chains 95 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 521 ARG Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain B residue 30 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.8148 > 50: distance: 3 - 6: 27.238 distance: 6 - 7: 58.815 distance: 7 - 8: 15.357 distance: 7 - 10: 57.215 distance: 8 - 9: 30.017 distance: 8 - 11: 20.188 distance: 9 - 32: 31.596 distance: 11 - 12: 36.177 distance: 12 - 13: 41.921 distance: 12 - 15: 13.349 distance: 13 - 14: 38.739 distance: 13 - 20: 23.917 distance: 14 - 37: 26.578 distance: 15 - 16: 21.794 distance: 16 - 17: 6.580 distance: 17 - 18: 8.453 distance: 17 - 19: 6.980 distance: 20 - 21: 42.166 distance: 21 - 22: 29.723 distance: 21 - 24: 23.055 distance: 22 - 23: 22.799 distance: 22 - 27: 28.582 distance: 24 - 25: 22.002 distance: 24 - 26: 23.601 distance: 27 - 28: 23.296 distance: 28 - 29: 7.071 distance: 28 - 31: 3.917 distance: 29 - 30: 15.589 distance: 29 - 32: 8.370 distance: 32 - 33: 24.021 distance: 33 - 34: 30.199 distance: 34 - 35: 22.810 distance: 34 - 37: 24.478 distance: 37 - 38: 25.779 distance: 38 - 39: 44.710 distance: 38 - 41: 30.120 distance: 39 - 40: 41.540 distance: 39 - 44: 33.098 distance: 41 - 42: 18.943 distance: 41 - 43: 11.689 distance: 44 - 45: 17.246 distance: 45 - 46: 11.766 distance: 45 - 48: 10.803 distance: 46 - 47: 25.641 distance: 46 - 53: 16.045 distance: 48 - 49: 5.716 distance: 49 - 50: 15.165 distance: 50 - 51: 17.663 distance: 50 - 52: 12.182 distance: 53 - 54: 13.172 distance: 54 - 55: 23.742 distance: 54 - 57: 27.764 distance: 55 - 56: 22.796 distance: 55 - 58: 17.596 distance: 58 - 59: 37.399 distance: 59 - 60: 41.140 distance: 60 - 61: 22.838 distance: 60 - 62: 28.609 distance: 62 - 63: 24.719 distance: 63 - 64: 7.964 distance: 63 - 66: 10.855 distance: 64 - 65: 19.314 distance: 64 - 70: 7.674 distance: 66 - 67: 14.101 distance: 67 - 68: 7.409 distance: 67 - 69: 5.371