Starting phenix.real_space_refine on Thu Mar 6 06:54:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iv5_35741/03_2025/8iv5_35741.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iv5_35741/03_2025/8iv5_35741.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iv5_35741/03_2025/8iv5_35741.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iv5_35741/03_2025/8iv5_35741.map" model { file = "/net/cci-nas-00/data/ceres_data/8iv5_35741/03_2025/8iv5_35741.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iv5_35741/03_2025/8iv5_35741.cif" } resolution = 3.77 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= 0.011 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 29 5.16 5 C 3221 2.51 5 N 857 2.21 5 O 989 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 5096 Number of models: 1 Model: "" Number of chains: 6 Chain: "G" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "L" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 836 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "H" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 921 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "B" 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': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "A" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 947 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 13.04, per 1000 atoms: 2.56 Number of scatterers: 5096 At special positions: 0 Unit cell: (113.588, 73.132, 79.356, 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 29 16.00 O 989 8.00 N 857 7.00 C 3221 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS G 336 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 379 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 480 " - pdb=" SG CYS G 488 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 98 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG C 1 " - " ASN G 343 " Time building additional restraints: 2.04 Conformation dependent library (CDL) restraints added in 812.3 milliseconds 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1176 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 14 sheets defined 6.5% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'G' and resid 337 through 343 removed outlier: 3.832A pdb=" N VAL G 341 " --> pdb=" O PRO G 337 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE G 342 " --> pdb=" O PHE G 338 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN G 343 " --> pdb=" O GLY G 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 337 through 343' Processing helix chain 'G' and resid 365 through 370 Processing helix chain 'G' and resid 403 through 407 removed outlier: 3.516A pdb=" N GLU G 406 " --> pdb=" O ARG G 403 " (cutoff:3.500A) Processing helix chain 'G' and resid 502 through 506 removed outlier: 3.520A pdb=" N GLN G 506 " --> pdb=" O VAL G 503 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 57 Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.599A pdb=" N ASP B 82 " --> pdb=" O GLU B 79 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE B 83 " --> pdb=" O THR B 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 79 through 83' Processing helix chain 'A' and resid 28 through 32 removed outlier: 4.028A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 removed outlier: 3.812A pdb=" N ARG A 65 " --> pdb=" O ASP A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 65' Processing sheet with id=AA1, first strand: chain 'G' and resid 354 through 358 removed outlier: 3.857A pdb=" N ASN G 354 " --> pdb=" O SER G 399 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER G 399 " --> pdb=" O ASN G 354 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'G' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 11 Processing sheet with id=AA5, first strand: chain 'L' and resid 18 through 23 removed outlier: 3.999A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.666A pdb=" N TYR L 49 " --> pdb=" O ASN L 53 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TRP L 35 " --> pdb=" O MET L 47 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.614A pdb=" N VAL H 12 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N MET H 34 " --> pdb=" O GLN H 50 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N GLN H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 17 through 23 removed outlier: 3.519A pdb=" N MET H 85 " --> pdb=" O MET H 18 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER H 80 " --> pdb=" O ASP H 75 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP H 75 " --> pdb=" O SER H 80 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 5 through 6 Processing sheet with id=AB1, first strand: chain 'B' and resid 19 through 20 removed outlier: 3.613A pdb=" N VAL B 19 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR B 72 " --> pdb=" O SER B 65 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 45 through 48 removed outlier: 6.905A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 3 through 6 removed outlier: 3.963A pdb=" N GLN A 3 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER A 25 " --> pdb=" O GLN A 3 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.727A pdb=" N GLU A 10 " --> pdb=" O THR A 116 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL A 37 " --> pdb=" O PHE A 95 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU A 34 " --> pdb=" O TRP A 50 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TRP A 50 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 18 through 20 removed outlier: 3.617A pdb=" N VAL A 18 " --> pdb=" O ILE A 83 " (cutoff:3.500A) 113 hydrogen bonds defined for protein. 264 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: 2.45 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1619 1.34 - 1.46: 1311 1.46 - 1.58: 2252 1.58 - 1.70: 0 1.70 - 1.82: 39 Bond restraints: 5221 Sorted by residual: bond pdb=" C GLN G 506 " pdb=" N PRO G 507 " ideal model delta sigma weight residual 1.333 1.356 -0.022 1.01e-02 9.80e+03 4.88e+00 bond pdb=" C5 BMA C 3 " pdb=" O5 BMA C 3 " ideal model delta sigma weight residual 1.417 1.451 -0.034 2.00e-02 2.50e+03 2.95e+00 bond pdb=" N ASN B 31 " pdb=" CA ASN B 31 " ideal model delta sigma weight residual 1.457 1.477 -0.019 1.29e-02 6.01e+03 2.25e+00 bond pdb=" CB TRP H 47 " pdb=" CG TRP H 47 " ideal model delta sigma weight residual 1.498 1.453 0.045 3.10e-02 1.04e+03 2.07e+00 bond pdb=" CA VAL H 48 " pdb=" CB VAL H 48 " ideal model delta sigma weight residual 1.545 1.532 0.013 9.10e-03 1.21e+04 1.94e+00 ... (remaining 5216 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 6832 2.18 - 4.36: 225 4.36 - 6.55: 21 6.55 - 8.73: 2 8.73 - 10.91: 2 Bond angle restraints: 7082 Sorted by residual: angle pdb=" C SER B 40 " pdb=" N HIS B 41 " pdb=" CA HIS B 41 " ideal model delta sigma weight residual 122.82 128.23 -5.41 1.42e+00 4.96e-01 1.45e+01 angle pdb=" N GLY G 404 " pdb=" CA GLY G 404 " pdb=" C GLY G 404 " ideal model delta sigma weight residual 112.49 116.54 -4.05 1.21e+00 6.83e-01 1.12e+01 angle pdb=" C SER L 76 " pdb=" N ASN L 77 " pdb=" CA ASN L 77 " ideal model delta sigma weight residual 122.82 127.52 -4.70 1.42e+00 4.96e-01 1.10e+01 angle pdb=" C SER B 30 " pdb=" N ASN B 31 " pdb=" CA ASN B 31 " ideal model delta sigma weight residual 121.54 127.54 -6.00 1.91e+00 2.74e-01 9.86e+00 angle pdb=" C GLY A 66 " pdb=" N ARG A 67 " pdb=" CA ARG A 67 " ideal model delta sigma weight residual 121.54 127.44 -5.90 1.91e+00 2.74e-01 9.56e+00 ... (remaining 7077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.02: 2822 20.02 - 40.03: 237 40.03 - 60.05: 28 60.05 - 80.07: 11 80.07 - 100.08: 4 Dihedral angle restraints: 3102 sinusoidal: 1251 harmonic: 1851 Sorted by residual: dihedral pdb=" CB CYS G 480 " pdb=" SG CYS G 480 " pdb=" SG CYS G 488 " pdb=" CB CYS G 488 " ideal model delta sinusoidal sigma weight residual -86.00 -133.64 47.64 1 1.00e+01 1.00e-02 3.13e+01 dihedral pdb=" CA CYS G 480 " pdb=" C CYS G 480 " pdb=" N ASN G 481 " pdb=" CA ASN G 481 " ideal model delta harmonic sigma weight residual 180.00 154.30 25.70 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA TYR A 60 " pdb=" C TYR A 60 " pdb=" N ASN A 61 " pdb=" CA ASN A 61 " ideal model delta harmonic sigma weight residual 180.00 155.27 24.73 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 3099 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 563 0.057 - 0.113: 155 0.113 - 0.170: 39 0.170 - 0.227: 6 0.227 - 0.284: 1 Chirality restraints: 764 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA TYR L 94 " pdb=" N TYR L 94 " pdb=" C TYR L 94 " pdb=" CB TYR L 94 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB ILE A 51 " pdb=" CA ILE A 51 " pdb=" CG1 ILE A 51 " pdb=" CG2 ILE A 51 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 761 not shown) Planarity restraints: 911 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR L 94 " -0.044 5.00e-02 4.00e+02 6.61e-02 7.00e+00 pdb=" N PRO L 95 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS G 462 " -0.037 5.00e-02 4.00e+02 5.52e-02 4.88e+00 pdb=" N PRO G 463 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO G 463 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO G 463 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 58 " -0.036 5.00e-02 4.00e+02 5.44e-02 4.74e+00 pdb=" N PRO L 59 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO L 59 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO L 59 " -0.030 5.00e-02 4.00e+02 ... (remaining 908 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1629 2.82 - 3.34: 4043 3.34 - 3.86: 7954 3.86 - 4.38: 8799 4.38 - 4.90: 15817 Nonbonded interactions: 38242 Sorted by model distance: nonbonded pdb=" OD2 ASP G 398 " pdb=" OH TYR G 423 " model vdw 2.297 3.040 nonbonded pdb=" O SER B 91 " pdb=" OG SER B 91 " model vdw 2.307 3.040 nonbonded pdb=" OD1 ASP A 90 " pdb=" OH TYR A 94 " model vdw 2.314 3.040 nonbonded pdb=" OG1 THR G 345 " pdb=" O ASN B 92 " model vdw 2.327 3.040 nonbonded pdb=" OG SER B 63 " pdb=" OG SER B 74 " model vdw 2.332 3.040 ... (remaining 38237 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=0.83 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 126.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 31.350 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 162.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 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 0.068 5221 Z= 0.456 Angle : 0.878 10.910 7082 Z= 0.494 Chirality : 0.057 0.284 764 Planarity : 0.007 0.066 910 Dihedral : 15.145 100.082 1905 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 0.91 % Allowed : 9.80 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.73 (0.29), residues: 635 helix: -5.19 (0.23), residues: 20 sheet: -2.11 (0.31), residues: 238 loop : -2.64 (0.27), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP G 436 HIS 0.003 0.001 HIS L 91 PHE 0.020 0.002 PHE B 62 TYR 0.022 0.003 TYR L 49 ARG 0.003 0.001 ARG G 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 154 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 466 ARG cc_start: 0.6802 (ptm160) cc_final: 0.5969 (ptm160) REVERT: G 472 ILE cc_start: 0.7949 (mm) cc_final: 0.7591 (mm) REVERT: G 493 GLN cc_start: 0.7198 (tt0) cc_final: 0.6725 (tm-30) REVERT: L 4 MET cc_start: 0.8176 (mmm) cc_final: 0.7958 (mmp) REVERT: L 19 VAL cc_start: 0.8552 (p) cc_final: 0.8208 (t) REVERT: L 26 SER cc_start: 0.7614 (m) cc_final: 0.7171 (m) REVERT: L 102 THR cc_start: 0.8308 (m) cc_final: 0.8092 (m) REVERT: H 35 ASP cc_start: 0.7719 (m-30) cc_final: 0.6547 (m-30) REVERT: H 50 GLN cc_start: 0.7769 (tt0) cc_final: 0.6865 (tt0) REVERT: H 54 LYS cc_start: 0.8345 (mtpt) cc_final: 0.7885 (tptt) REVERT: H 73 SER cc_start: 0.7672 (m) cc_final: 0.7458 (p) REVERT: B 40 SER cc_start: 0.7934 (t) cc_final: 0.7721 (t) REVERT: B 61 ARG cc_start: 0.6137 (ptt-90) cc_final: 0.5591 (ptt-90) REVERT: B 70 ASP cc_start: 0.7105 (m-30) cc_final: 0.6324 (m-30) REVERT: B 105 GLU cc_start: 0.7443 (pt0) cc_final: 0.7241 (pt0) REVERT: A 10 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7310 (mm-30) REVERT: A 19 LYS cc_start: 0.7808 (ttmt) cc_final: 0.7351 (tttp) REVERT: A 62 ASP cc_start: 0.7672 (m-30) cc_final: 0.7434 (m-30) REVERT: A 65 ARG cc_start: 0.7007 (ttp-110) cc_final: 0.6655 (mtm110) REVERT: A 87 LYS cc_start: 0.7568 (mttt) cc_final: 0.7239 (mtmt) outliers start: 5 outliers final: 5 residues processed: 158 average time/residue: 0.2461 time to fit residues: 48.4098 Evaluate side-chains 137 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 132 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain H residue 115 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 370 ASN ** G 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 440 ASN G 460 ASN L 8 GLN L 37 GLN L 38 GLN L 77 ASN ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN A 39 GLN A 52 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.120481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.102316 restraints weight = 7942.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.104678 restraints weight = 5363.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.106552 restraints weight = 4087.248| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 5221 Z= 0.308 Angle : 0.626 5.948 7082 Z= 0.334 Chirality : 0.045 0.160 764 Planarity : 0.005 0.053 910 Dihedral : 8.670 57.620 773 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.27 % Allowed : 18.33 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.31), residues: 635 helix: -4.73 (0.43), residues: 26 sheet: -1.82 (0.32), residues: 254 loop : -2.31 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 436 HIS 0.002 0.001 HIS B 41 PHE 0.017 0.002 PHE B 62 TYR 0.023 0.002 TYR L 49 ARG 0.003 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 417 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7857 (tttp) REVERT: G 466 ARG cc_start: 0.8402 (ptm160) cc_final: 0.7924 (ptm160) REVERT: G 472 ILE cc_start: 0.9251 (mm) cc_final: 0.9039 (mm) REVERT: L 104 LEU cc_start: 0.6855 (OUTLIER) cc_final: 0.6467 (tt) REVERT: B 61 ARG cc_start: 0.8280 (ptt-90) cc_final: 0.8020 (ptt-90) REVERT: A 65 ARG cc_start: 0.7561 (ttp-110) cc_final: 0.7340 (ttm110) outliers start: 18 outliers final: 15 residues processed: 151 average time/residue: 0.1946 time to fit residues: 36.5356 Evaluate side-chains 144 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 417 LYS Chi-restraints excluded: chain G residue 501 ASN Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 49 optimal weight: 0.2980 chunk 57 optimal weight: 0.0000 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 HIS ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.120689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.102500 restraints weight = 7933.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.105002 restraints weight = 5366.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.106805 restraints weight = 4059.502| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5221 Z= 0.208 Angle : 0.574 6.021 7082 Z= 0.304 Chirality : 0.044 0.154 764 Planarity : 0.004 0.047 910 Dihedral : 6.575 35.196 770 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 5.44 % Allowed : 19.60 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.31), residues: 635 helix: -4.34 (0.60), residues: 26 sheet: -1.51 (0.32), residues: 249 loop : -2.20 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 436 HIS 0.003 0.001 HIS B 41 PHE 0.012 0.001 PHE L 62 TYR 0.020 0.001 TYR A 80 ARG 0.005 0.000 ARG G 355 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: G 466 ARG cc_start: 0.8393 (ptm160) cc_final: 0.7841 (ptm160) REVERT: G 472 ILE cc_start: 0.9260 (mm) cc_final: 0.9054 (mm) REVERT: L 104 LEU cc_start: 0.6752 (OUTLIER) cc_final: 0.6289 (tt) REVERT: B 61 ARG cc_start: 0.8182 (ptt-90) cc_final: 0.7824 (ptt90) REVERT: B 90 GLN cc_start: 0.9338 (pp30) cc_final: 0.9116 (pp30) REVERT: B 93 THR cc_start: 0.9548 (OUTLIER) cc_final: 0.9339 (m) outliers start: 30 outliers final: 18 residues processed: 151 average time/residue: 0.1690 time to fit residues: 32.3402 Evaluate side-chains 147 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 501 ASN Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 51 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 4 optimal weight: 0.0170 chunk 34 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 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 = 0.3299 r_free = 0.3299 target = 0.119237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.100851 restraints weight = 8161.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.103301 restraints weight = 5484.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.105071 restraints weight = 4170.357| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3112 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5221 Z= 0.247 Angle : 0.584 6.002 7082 Z= 0.306 Chirality : 0.044 0.151 764 Planarity : 0.004 0.045 910 Dihedral : 6.061 33.861 770 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 5.08 % Allowed : 21.23 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.31), residues: 635 helix: -4.16 (0.68), residues: 26 sheet: -1.38 (0.32), residues: 248 loop : -2.08 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 436 HIS 0.002 0.001 HIS B 41 PHE 0.015 0.001 PHE B 62 TYR 0.016 0.002 TYR G 449 ARG 0.005 0.000 ARG G 408 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.574 Fit side-chains revert: symmetry clash REVERT: G 466 ARG cc_start: 0.8426 (ptm160) cc_final: 0.7829 (ptm160) REVERT: G 472 ILE cc_start: 0.9249 (mm) cc_final: 0.9027 (mm) REVERT: B 61 ARG cc_start: 0.8253 (ptt-90) cc_final: 0.7810 (ptt90) REVERT: A 80 TYR cc_start: 0.8541 (m-10) cc_final: 0.8246 (m-10) outliers start: 28 outliers final: 24 residues processed: 143 average time/residue: 0.1869 time to fit residues: 33.6484 Evaluate side-chains 147 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 349 SER Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 501 ASN Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain H residue 5 GLU Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 74 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 28 optimal weight: 0.0570 chunk 17 optimal weight: 0.3980 chunk 18 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 34 optimal weight: 0.0870 chunk 12 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 14 optimal weight: 0.3980 overall best weight: 0.3076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 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 = 0.3327 r_free = 0.3327 target = 0.121560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.103482 restraints weight = 7997.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.106028 restraints weight = 5357.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.107688 restraints weight = 4028.433| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5221 Z= 0.159 Angle : 0.552 6.124 7082 Z= 0.287 Chirality : 0.043 0.150 764 Planarity : 0.004 0.047 910 Dihedral : 5.545 33.915 770 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 4.17 % Allowed : 22.50 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.32), residues: 635 helix: -4.07 (0.73), residues: 26 sheet: -1.06 (0.33), residues: 246 loop : -2.01 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 436 HIS 0.002 0.001 HIS L 91 PHE 0.016 0.001 PHE L 62 TYR 0.016 0.001 TYR G 449 ARG 0.007 0.000 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 466 ARG cc_start: 0.8360 (ptm160) cc_final: 0.7800 (ptm160) REVERT: G 472 ILE cc_start: 0.9251 (mm) cc_final: 0.9012 (mm) REVERT: L 107 LYS cc_start: 0.6328 (mtmm) cc_final: 0.5359 (mmtt) REVERT: B 61 ARG cc_start: 0.8127 (ptt-90) cc_final: 0.7670 (ptt90) outliers start: 23 outliers final: 18 residues processed: 144 average time/residue: 0.1756 time to fit residues: 32.1517 Evaluate side-chains 144 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 349 SER Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 501 ASN Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 74 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 39 optimal weight: 0.0670 chunk 60 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 1 optimal weight: 0.4980 chunk 18 optimal weight: 0.0070 chunk 54 optimal weight: 1.9990 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.121661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.103745 restraints weight = 7971.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.106189 restraints weight = 5365.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.107958 restraints weight = 4071.548| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5221 Z= 0.170 Angle : 0.543 6.095 7082 Z= 0.284 Chirality : 0.043 0.152 764 Planarity : 0.004 0.048 910 Dihedral : 5.385 32.988 770 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 5.26 % Allowed : 22.87 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.32), residues: 635 helix: -4.04 (0.72), residues: 26 sheet: -0.88 (0.33), residues: 245 loop : -1.87 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 436 HIS 0.002 0.001 HIS L 91 PHE 0.030 0.001 PHE H 70 TYR 0.015 0.001 TYR G 449 ARG 0.007 0.000 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 466 ARG cc_start: 0.8368 (ptm160) cc_final: 0.7785 (ptm160) REVERT: G 472 ILE cc_start: 0.9253 (mm) cc_final: 0.9015 (mm) REVERT: L 107 LYS cc_start: 0.6330 (mtmm) cc_final: 0.5407 (mmtt) REVERT: B 61 ARG cc_start: 0.8141 (ptt-90) cc_final: 0.7632 (ptt90) REVERT: A 65 ARG cc_start: 0.8025 (ttm-80) cc_final: 0.7596 (ttm-80) outliers start: 29 outliers final: 25 residues processed: 146 average time/residue: 0.1895 time to fit residues: 35.1986 Evaluate side-chains 150 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 349 SER Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 483 VAL Chi-restraints excluded: chain G residue 501 ASN Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain H residue 5 GLU Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 74 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 50 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 7 optimal weight: 0.0050 chunk 25 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 56 optimal weight: 0.1980 chunk 27 optimal weight: 2.9990 chunk 49 optimal weight: 0.0770 chunk 29 optimal weight: 5.9990 overall best weight: 0.3752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 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 = 0.3331 r_free = 0.3331 target = 0.121919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.103380 restraints weight = 7883.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.106002 restraints weight = 5226.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.107904 restraints weight = 3909.198| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3169 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5221 Z= 0.172 Angle : 0.540 5.600 7082 Z= 0.283 Chirality : 0.043 0.152 764 Planarity : 0.004 0.050 910 Dihedral : 5.265 32.351 770 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 5.26 % Allowed : 23.05 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.32), residues: 635 helix: -3.54 (0.75), residues: 32 sheet: -0.81 (0.33), residues: 249 loop : -1.66 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 436 HIS 0.002 0.000 HIS L 91 PHE 0.024 0.001 PHE A 64 TYR 0.016 0.001 TYR G 453 ARG 0.006 0.000 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 466 ARG cc_start: 0.8363 (ptm160) cc_final: 0.7771 (ptm160) REVERT: G 472 ILE cc_start: 0.9253 (mm) cc_final: 0.9019 (mm) REVERT: L 107 LYS cc_start: 0.6418 (mtmm) cc_final: 0.5446 (mmtt) REVERT: B 61 ARG cc_start: 0.8168 (ptt-90) cc_final: 0.7614 (ptt90) REVERT: A 65 ARG cc_start: 0.7994 (ttm-80) cc_final: 0.7588 (ttm-80) outliers start: 29 outliers final: 25 residues processed: 143 average time/residue: 0.1798 time to fit residues: 32.5633 Evaluate side-chains 147 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 349 SER Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 483 VAL Chi-restraints excluded: chain G residue 501 ASN Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain H residue 5 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 74 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- 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: 69.2198 > 50: distance: 14 - 19: 22.059 distance: 19 - 20: 26.848 distance: 19 - 184: 21.914 distance: 20 - 21: 19.756 distance: 20 - 23: 43.287 distance: 21 - 22: 33.633 distance: 22 - 181: 33.044 distance: 23 - 24: 27.520 distance: 23 - 25: 46.636 distance: 24 - 26: 27.846 distance: 27 - 28: 18.169 distance: 28 - 29: 22.298 distance: 28 - 31: 20.709 distance: 29 - 38: 68.735 distance: 31 - 32: 16.426 distance: 32 - 33: 23.199 distance: 34 - 35: 40.295 distance: 35 - 37: 56.425 distance: 38 - 39: 40.664 distance: 39 - 40: 39.332 distance: 40 - 41: 36.726 distance: 41 - 59: 37.947 distance: 46 - 47: 14.406 distance: 47 - 48: 40.100 distance: 47 - 49: 27.308 distance: 50 - 51: 18.259 distance: 51 - 52: 9.930 distance: 51 - 54: 43.828 distance: 52 - 53: 21.707 distance: 52 - 59: 7.912 distance: 55 - 56: 51.484 distance: 56 - 57: 26.592 distance: 56 - 58: 32.664 distance: 60 - 61: 42.220 distance: 61 - 62: 13.173 distance: 61 - 66: 13.137 distance: 63 - 64: 39.843 distance: 63 - 65: 38.949 distance: 66 - 67: 8.118 distance: 67 - 68: 11.504 distance: 67 - 70: 41.961 distance: 68 - 69: 6.812 distance: 70 - 71: 22.637 distance: 71 - 72: 48.739 distance: 72 - 73: 23.491 distance: 73 - 74: 53.772 distance: 74 - 75: 39.996 distance: 74 - 76: 3.669 distance: 78 - 79: 45.846 distance: 78 - 81: 40.108 distance: 79 - 80: 24.791 distance: 79 - 86: 26.234 distance: 81 - 82: 11.350 distance: 82 - 83: 24.335 distance: 83 - 84: 3.129 distance: 83 - 85: 43.013 distance: 87 - 90: 38.661 distance: 88 - 89: 20.597 distance: 88 - 94: 40.521 distance: 90 - 92: 57.102 distance: 95 - 96: 40.858 distance: 95 - 98: 39.902 distance: 96 - 99: 33.977