Starting phenix.real_space_refine on Sat May 10 05:02:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iv4_35740/05_2025/8iv4_35740.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iv4_35740/05_2025/8iv4_35740.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iv4_35740/05_2025/8iv4_35740.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iv4_35740/05_2025/8iv4_35740.map" model { file = "/net/cci-nas-00/data/ceres_data/8iv4_35740/05_2025/8iv4_35740.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iv4_35740/05_2025/8iv4_35740.cif" } resolution = 3.59 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= 0.013 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 33 5.16 5 C 3173 2.51 5 N 841 2.21 5 O 980 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 5027 Number of models: 1 Model: "" Number of chains: 6 Chain: "L" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 788 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 100} Chain: "H" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 918 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "B" 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: "A" 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: "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: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.26, per 1000 atoms: 0.45 Number of scatterers: 5027 At special positions: 0 Unit cell: (86.358, 66.908, 109.698, 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 33 16.00 O 980 8.00 N 841 7.00 C 3173 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 98 " distance=2.03 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 391 " - pdb=" SG CYS G 525 " distance=2.03 Simple disulfide: pdb=" SG CYS G 480 " - pdb=" SG CYS G 488 " 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-ASN " NAG C 1 " - " ASN G 343 " Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 554.0 milliseconds 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1172 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 12 sheets defined 6.2% alpha, 33.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.002A pdb=" N THR H 31 " --> pdb=" O SER H 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.801A pdb=" N ASP B 82 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU B 83 " --> pdb=" O CYS B 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 79 through 83' Processing helix chain 'A' and resid 53 through 57 Processing helix chain 'G' and resid 349 through 353 removed outlier: 3.918A pdb=" N TRP G 353 " --> pdb=" O VAL G 350 " (cutoff:3.500A) Processing helix chain 'G' and resid 364 through 370 removed outlier: 3.923A pdb=" N LEU G 368 " --> pdb=" O ASP G 364 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 410 removed outlier: 4.482A pdb=" N ARG G 408 " --> pdb=" O ASP G 405 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE G 410 " --> pdb=" O VAL G 407 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 422 removed outlier: 3.698A pdb=" N TYR G 421 " --> pdb=" O LYS G 417 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.745A pdb=" N SER L 7 " --> pdb=" O THR L 22 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N THR L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N THR L 68 " --> pdb=" O VAL L 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.532A pdb=" N GLU L 102 " --> pdb=" O MET L 11 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 52 through 53 removed outlier: 3.560A pdb=" N TYR L 48 " --> pdb=" O ASN L 52 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N VAL L 45 " --> pdb=" O GLN L 36 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLN L 36 " --> pdb=" O VAL L 45 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.521A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP H 73 " --> pdb=" O THR H 78 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.535A pdb=" N VAL H 12 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR H 115 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TYR H 94 " --> pdb=" O THR H 115 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N THR H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LEU H 45 " --> pdb=" O THR H 40 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.535A pdb=" N VAL H 12 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR H 115 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TYR H 94 " --> pdb=" O THR H 115 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 5 Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.565A pdb=" N GLU B 105 " --> pdb=" O MET B 11 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N TYR B 49 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP B 35 " --> pdb=" O MET B 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AB1, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.519A pdb=" N GLY A 10 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N MET A 34 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N GLN A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 354 through 358 Processing sheet with id=AB3, first strand: chain 'G' and resid 452 through 454 146 hydrogen bonds defined for protein. 357 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: 1.38 Time building geometry restraints manager: 1.35 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: 1593 1.34 - 1.46: 1294 1.46 - 1.58: 2212 1.58 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 5147 Sorted by residual: bond pdb=" C LEU G 335 " pdb=" N CYS G 336 " ideal model delta sigma weight residual 1.331 1.269 0.062 2.07e-02 2.33e+03 8.86e+00 bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.54e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 4.97e+00 bond pdb=" N TYR G 473 " pdb=" CA TYR G 473 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.29e-02 6.01e+03 4.31e+00 bond pdb=" N CYS G 488 " pdb=" CA CYS G 488 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.29e-02 6.01e+03 3.10e+00 ... (remaining 5142 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 6609 1.69 - 3.39: 323 3.39 - 5.08: 29 5.08 - 6.77: 10 6.77 - 8.47: 4 Bond angle restraints: 6975 Sorted by residual: angle pdb=" C SER L 49 " pdb=" N THR L 50 " pdb=" CA THR L 50 " ideal model delta sigma weight residual 121.54 129.08 -7.54 1.91e+00 2.74e-01 1.56e+01 angle pdb=" C SER L 92 " pdb=" N TRP L 93 " pdb=" CA TRP L 93 " ideal model delta sigma weight residual 121.54 128.98 -7.44 1.91e+00 2.74e-01 1.52e+01 angle pdb=" N TYR B 94 " pdb=" CA TYR B 94 " pdb=" C TYR B 94 " ideal model delta sigma weight residual 109.81 118.28 -8.47 2.21e+00 2.05e-01 1.47e+01 angle pdb=" C GLN L 89 " pdb=" N TRP L 90 " pdb=" CA TRP L 90 " ideal model delta sigma weight residual 120.63 126.24 -5.61 1.61e+00 3.86e-01 1.21e+01 angle pdb=" N GLN A 111 " pdb=" CA GLN A 111 " pdb=" C GLN A 111 " ideal model delta sigma weight residual 114.56 110.26 4.30 1.27e+00 6.20e-01 1.14e+01 ... (remaining 6970 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 2744 17.91 - 35.81: 253 35.81 - 53.72: 45 53.72 - 71.62: 4 71.62 - 89.53: 5 Dihedral angle restraints: 3051 sinusoidal: 1201 harmonic: 1850 Sorted by residual: dihedral pdb=" CA ASN G 487 " pdb=" C ASN G 487 " pdb=" N CYS G 488 " pdb=" CA CYS G 488 " ideal model delta harmonic sigma weight residual -180.00 -131.59 -48.41 0 5.00e+00 4.00e-02 9.38e+01 dihedral pdb=" CA CYS G 361 " pdb=" C CYS G 361 " pdb=" N VAL G 362 " pdb=" CA VAL G 362 " ideal model delta harmonic sigma weight residual 180.00 157.79 22.21 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CB CYS G 336 " pdb=" SG CYS G 336 " pdb=" SG CYS G 361 " pdb=" CB CYS G 361 " ideal model delta sinusoidal sigma weight residual 93.00 58.47 34.53 1 1.00e+01 1.00e-02 1.69e+01 ... (remaining 3048 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 514 0.047 - 0.094: 171 0.094 - 0.141: 56 0.141 - 0.188: 9 0.188 - 0.235: 4 Chirality restraints: 754 Sorted by residual: chirality pdb=" CB VAL H 48 " pdb=" CA VAL H 48 " pdb=" CG1 VAL H 48 " pdb=" CG2 VAL H 48 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB THR A 28 " pdb=" CA THR A 28 " pdb=" OG1 THR A 28 " pdb=" CG2 THR A 28 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA TYR B 94 " pdb=" N TYR B 94 " pdb=" C TYR B 94 " pdb=" CB TYR B 94 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 751 not shown) Planarity restraints: 892 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN G 487 " 0.016 2.00e-02 2.50e+03 3.17e-02 1.01e+01 pdb=" C ASN G 487 " -0.055 2.00e-02 2.50e+03 pdb=" O ASN G 487 " 0.021 2.00e-02 2.50e+03 pdb=" N CYS G 488 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B 94 " -0.046 5.00e-02 4.00e+02 6.91e-02 7.63e+00 pdb=" N PRO B 95 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 95 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 95 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA G 520 " 0.042 5.00e-02 4.00e+02 6.33e-02 6.40e+00 pdb=" N PRO G 521 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO G 521 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO G 521 " 0.035 5.00e-02 4.00e+02 ... (remaining 889 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 1626 2.83 - 3.35: 3861 3.35 - 3.87: 8003 3.87 - 4.38: 8760 4.38 - 4.90: 16095 Nonbonded interactions: 38345 Sorted by model distance: nonbonded pdb=" O SER G 438 " pdb=" OG SER G 438 " model vdw 2.315 3.040 nonbonded pdb=" O SER H 30 " pdb=" OG SER H 30 " model vdw 2.327 3.040 nonbonded pdb=" OH TYR H 59 " pdb=" OH TYR H 103 " model vdw 2.336 3.040 nonbonded pdb=" O ARG H 67 " pdb=" OG SER H 84 " model vdw 2.354 3.040 nonbonded pdb=" OG SER G 438 " pdb=" OD2 ASP G 442 " model vdw 2.361 3.040 ... (remaining 38340 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: 39.250 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 12.000 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6501 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 5157 Z= 0.258 Angle : 0.853 8.871 6997 Z= 0.495 Chirality : 0.054 0.235 754 Planarity : 0.007 0.069 891 Dihedral : 14.005 89.529 1855 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.55 % Allowed : 6.96 % Favored : 92.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.00 (0.27), residues: 634 helix: -4.95 (0.21), residues: 21 sheet: -1.94 (0.31), residues: 250 loop : -3.14 (0.24), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 47 HIS 0.004 0.001 HIS B 91 PHE 0.022 0.002 PHE L 46 TYR 0.026 0.002 TYR B 94 ARG 0.001 0.000 ARG G 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00084 ( 1) link_NAG-ASN : angle 6.51442 ( 3) link_BETA1-4 : bond 0.01097 ( 1) link_BETA1-4 : angle 1.24981 ( 3) hydrogen bonds : bond 0.27686 ( 144) hydrogen bonds : angle 10.62234 ( 357) SS BOND : bond 0.00296 ( 8) SS BOND : angle 0.84826 ( 16) covalent geometry : bond 0.00550 ( 5147) covalent geometry : angle 0.84205 ( 6975) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 127 time to evaluate : 0.492 Fit side-chains REVERT: L 11 MET cc_start: 0.7400 (mtt) cc_final: 0.6839 (mtt) REVERT: L 19 ILE cc_start: 0.8245 (tt) cc_final: 0.8027 (tt) REVERT: L 32 MET cc_start: 0.7935 (tpp) cc_final: 0.7538 (tpp) REVERT: L 90 TRP cc_start: 0.7295 (t60) cc_final: 0.7030 (t60) REVERT: H 3 MET cc_start: 0.6729 (mtm) cc_final: 0.5999 (tpt) REVERT: H 19 LYS cc_start: 0.7516 (tttt) cc_final: 0.7029 (tttm) REVERT: H 82 GLN cc_start: 0.7352 (pp30) cc_final: 0.7110 (pp30) REVERT: H 93 MET cc_start: 0.6589 (ttm) cc_final: 0.6235 (ttm) REVERT: H 109 ASP cc_start: 0.8068 (m-30) cc_final: 0.7447 (m-30) REVERT: B 1 ASP cc_start: 0.7827 (p0) cc_final: 0.7625 (p0) REVERT: B 4 MET cc_start: 0.6457 (mmm) cc_final: 0.5943 (mmt) REVERT: B 47 MET cc_start: 0.7245 (mmp) cc_final: 0.6926 (mmp) REVERT: B 52 SER cc_start: 0.8365 (t) cc_final: 0.8140 (m) REVERT: B 54 ARG cc_start: 0.8177 (ttm110) cc_final: 0.7763 (ttp80) REVERT: B 79 GLN cc_start: 0.7684 (mm-40) cc_final: 0.7432 (mm110) REVERT: B 82 ASP cc_start: 0.8596 (m-30) cc_final: 0.8362 (m-30) REVERT: A 18 MET cc_start: 0.6312 (ttm) cc_final: 0.6019 (ttt) REVERT: A 19 LYS cc_start: 0.7633 (tttt) cc_final: 0.6874 (tttp) REVERT: A 35 ASP cc_start: 0.6952 (m-30) cc_final: 0.6541 (m-30) REVERT: A 50 GLN cc_start: 0.7547 (tt0) cc_final: 0.6930 (tt0) REVERT: A 69 ARG cc_start: 0.7395 (mtm110) cc_final: 0.7149 (mtp180) REVERT: A 108 PHE cc_start: 0.7478 (t80) cc_final: 0.7176 (t80) REVERT: G 347 PHE cc_start: 0.8147 (m-10) cc_final: 0.7861 (m-80) REVERT: G 369 TYR cc_start: 0.8841 (t80) cc_final: 0.8477 (t80) REVERT: G 442 ASP cc_start: 0.8779 (m-30) cc_final: 0.8098 (m-30) outliers start: 3 outliers final: 1 residues processed: 128 average time/residue: 0.1880 time to fit residues: 29.7952 Evaluate side-chains 103 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 31 optimal weight: 0.0980 chunk 25 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 36 optimal weight: 0.4980 chunk 56 optimal weight: 0.4980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.135186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.114601 restraints weight = 6645.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.118642 restraints weight = 3455.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.121441 restraints weight = 2240.695| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3504 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3503 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5157 Z= 0.146 Angle : 0.592 7.006 6997 Z= 0.313 Chirality : 0.044 0.150 754 Planarity : 0.005 0.063 891 Dihedral : 6.192 69.317 752 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.26 % Favored : 92.59 % Rotamer: Outliers : 2.93 % Allowed : 10.62 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.22 (0.29), residues: 634 helix: -4.30 (0.47), residues: 15 sheet: -1.47 (0.30), residues: 257 loop : -2.62 (0.27), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 436 HIS 0.002 0.001 HIS B 91 PHE 0.015 0.001 PHE L 46 TYR 0.016 0.001 TYR B 94 ARG 0.005 0.000 ARG G 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00583 ( 1) link_NAG-ASN : angle 4.41923 ( 3) link_BETA1-4 : bond 0.01038 ( 1) link_BETA1-4 : angle 1.23528 ( 3) hydrogen bonds : bond 0.03764 ( 144) hydrogen bonds : angle 6.98286 ( 357) SS BOND : bond 0.00283 ( 8) SS BOND : angle 1.04257 ( 16) covalent geometry : bond 0.00329 ( 5147) covalent geometry : angle 0.58296 ( 6975) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: L 18 GLU cc_start: 0.7590 (pp20) cc_final: 0.7356 (pp20) REVERT: L 32 MET cc_start: 0.8602 (tpp) cc_final: 0.8084 (tpp) REVERT: L 66 SER cc_start: 0.8667 (p) cc_final: 0.8058 (m) REVERT: L 90 TRP cc_start: 0.8338 (t60) cc_final: 0.7664 (t60) REVERT: H 19 LYS cc_start: 0.8485 (tttt) cc_final: 0.8146 (tttm) REVERT: H 105 ASP cc_start: 0.8873 (p0) cc_final: 0.8542 (p0) REVERT: B 42 GLN cc_start: 0.8159 (mm-40) cc_final: 0.7866 (mt0) REVERT: A 3 LYS cc_start: 0.8552 (pptt) cc_final: 0.8280 (pttp) REVERT: A 19 LYS cc_start: 0.8539 (tttt) cc_final: 0.8102 (tttp) outliers start: 16 outliers final: 11 residues processed: 120 average time/residue: 0.2602 time to fit residues: 38.8557 Evaluate side-chains 112 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain G residue 375 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 49 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 HIS A 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.125075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.104434 restraints weight = 6842.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.108069 restraints weight = 3743.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.110480 restraints weight = 2500.535| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3459 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3459 r_free = 0.3459 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3459 r_free = 0.3459 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3459 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 5157 Z= 0.202 Angle : 0.616 8.962 6997 Z= 0.322 Chirality : 0.045 0.159 754 Planarity : 0.005 0.059 891 Dihedral : 6.036 59.501 752 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 5.68 % Allowed : 12.27 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.64 (0.30), residues: 634 helix: -3.75 (0.68), residues: 15 sheet: -0.95 (0.32), residues: 245 loop : -2.32 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 33 HIS 0.002 0.001 HIS L 88 PHE 0.010 0.001 PHE L 46 TYR 0.019 0.002 TYR B 94 ARG 0.005 0.001 ARG G 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00128 ( 1) link_NAG-ASN : angle 4.67640 ( 3) link_BETA1-4 : bond 0.00742 ( 1) link_BETA1-4 : angle 0.60941 ( 3) hydrogen bonds : bond 0.03643 ( 144) hydrogen bonds : angle 6.35124 ( 357) SS BOND : bond 0.00298 ( 8) SS BOND : angle 1.12290 ( 16) covalent geometry : bond 0.00470 ( 5147) covalent geometry : angle 0.60723 ( 6975) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 0.533 Fit side-chains REVERT: L 18 GLU cc_start: 0.7835 (pp20) cc_final: 0.7521 (pp20) REVERT: L 32 MET cc_start: 0.8655 (tpp) cc_final: 0.8102 (tpp) REVERT: L 66 SER cc_start: 0.8768 (p) cc_final: 0.8250 (m) REVERT: H 19 LYS cc_start: 0.8543 (tttt) cc_final: 0.8168 (tttm) REVERT: H 105 ASP cc_start: 0.8963 (p0) cc_final: 0.8750 (p0) REVERT: B 4 MET cc_start: 0.8144 (mmm) cc_final: 0.6629 (mmm) REVERT: B 42 GLN cc_start: 0.8295 (mm-40) cc_final: 0.8016 (mt0) REVERT: A 3 LYS cc_start: 0.8400 (pptt) cc_final: 0.8072 (pttp) REVERT: A 18 MET cc_start: 0.7815 (ttt) cc_final: 0.7567 (ttt) REVERT: A 19 LYS cc_start: 0.8596 (tttt) cc_final: 0.8109 (ttmm) REVERT: G 369 TYR cc_start: 0.8785 (t80) cc_final: 0.8520 (t80) REVERT: G 503 VAL cc_start: 0.9300 (OUTLIER) cc_final: 0.8902 (t) outliers start: 31 outliers final: 24 residues processed: 125 average time/residue: 0.1862 time to fit residues: 29.1627 Evaluate side-chains 130 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 353 TRP Chi-restraints excluded: chain G residue 361 CYS Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 442 ASP Chi-restraints excluded: chain G residue 503 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 50 optimal weight: 0.4980 chunk 53 optimal weight: 0.9980 chunk 48 optimal weight: 0.0030 chunk 1 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.147819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.128001 restraints weight = 6708.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.131701 restraints weight = 3777.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.134227 restraints weight = 2573.498| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3391 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3391 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5157 Z= 0.167 Angle : 0.574 6.862 6997 Z= 0.302 Chirality : 0.045 0.160 754 Planarity : 0.005 0.058 891 Dihedral : 5.849 51.198 752 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 5.86 % Allowed : 15.57 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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 (0.31), residues: 634 helix: -3.14 (0.93), residues: 15 sheet: -0.80 (0.32), residues: 247 loop : -2.08 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 33 HIS 0.004 0.001 HIS A 58 PHE 0.009 0.001 PHE A 70 TYR 0.025 0.002 TYR H 32 ARG 0.005 0.000 ARG G 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00474 ( 1) link_NAG-ASN : angle 3.70708 ( 3) link_BETA1-4 : bond 0.00326 ( 1) link_BETA1-4 : angle 0.88786 ( 3) hydrogen bonds : bond 0.03194 ( 144) hydrogen bonds : angle 5.97663 ( 357) SS BOND : bond 0.00234 ( 8) SS BOND : angle 0.96425 ( 16) covalent geometry : bond 0.00392 ( 5147) covalent geometry : angle 0.56788 ( 6975) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 106 time to evaluate : 0.529 Fit side-chains REVERT: L 18 GLU cc_start: 0.7621 (pp20) cc_final: 0.7392 (pp20) REVERT: L 32 MET cc_start: 0.8598 (tpp) cc_final: 0.8046 (tpp) REVERT: L 66 SER cc_start: 0.8781 (p) cc_final: 0.8208 (m) REVERT: H 19 LYS cc_start: 0.8488 (tttt) cc_final: 0.8063 (tttm) REVERT: B 42 GLN cc_start: 0.8189 (mm-40) cc_final: 0.7950 (mt0) REVERT: A 3 LYS cc_start: 0.8492 (pptt) cc_final: 0.8119 (pttp) REVERT: A 19 LYS cc_start: 0.8597 (tttt) cc_final: 0.8181 (tttp) REVERT: G 369 TYR cc_start: 0.8635 (t80) cc_final: 0.8387 (t80) outliers start: 32 outliers final: 24 residues processed: 123 average time/residue: 0.1749 time to fit residues: 27.1044 Evaluate side-chains 128 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 353 TRP Chi-restraints excluded: chain G residue 361 CYS Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 442 ASP Chi-restraints excluded: chain G residue 478 THR Chi-restraints excluded: chain G residue 511 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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: 55.3059 > 50: distance: 73 - 94: 8.940 distance: 90 - 94: 9.385 distance: 94 - 95: 21.748 distance: 95 - 96: 7.735 distance: 95 - 98: 10.582 distance: 96 - 97: 7.256 distance: 96 - 102: 15.624 distance: 98 - 99: 13.311 distance: 99 - 100: 5.408 distance: 99 - 101: 8.192 distance: 102 - 103: 8.925 distance: 103 - 104: 10.999 distance: 103 - 106: 12.066 distance: 104 - 105: 21.854 distance: 104 - 114: 18.190 distance: 106 - 107: 6.003 distance: 107 - 108: 13.275 distance: 107 - 109: 12.474 distance: 109 - 111: 9.388 distance: 110 - 112: 8.250 distance: 111 - 112: 8.325 distance: 112 - 113: 17.218 distance: 114 - 115: 12.662 distance: 115 - 116: 19.647 distance: 115 - 118: 20.992 distance: 116 - 117: 11.969 distance: 116 - 123: 23.804 distance: 118 - 119: 13.291 distance: 119 - 120: 27.429 distance: 120 - 121: 23.626 distance: 121 - 122: 12.648 distance: 123 - 124: 17.661 distance: 124 - 125: 17.036 distance: 124 - 127: 18.471 distance: 125 - 126: 36.154 distance: 125 - 131: 9.906 distance: 127 - 128: 10.076 distance: 128 - 129: 33.467 distance: 128 - 130: 39.529 distance: 131 - 132: 10.697 distance: 131 - 137: 32.202 distance: 132 - 133: 14.398 distance: 132 - 135: 13.530 distance: 133 - 134: 17.657 distance: 133 - 138: 17.787 distance: 135 - 136: 31.775 distance: 136 - 137: 37.397 distance: 139 - 142: 8.313 distance: 140 - 141: 23.277 distance: 140 - 146: 25.880 distance: 142 - 143: 9.438 distance: 143 - 144: 10.111 distance: 143 - 145: 4.476 distance: 146 - 147: 7.930 distance: 147 - 148: 4.914 distance: 147 - 150: 8.238 distance: 148 - 154: 3.438 distance: 150 - 151: 11.812 distance: 151 - 152: 9.018 distance: 151 - 153: 15.062 distance: 154 - 155: 8.243 distance: 155 - 156: 3.317 distance: 155 - 158: 6.263 distance: 156 - 157: 16.968 distance: 156 - 165: 12.108 distance: 158 - 159: 9.799 distance: 159 - 160: 5.661 distance: 159 - 161: 5.791 distance: 160 - 162: 5.342 distance: 161 - 163: 3.836 distance: 162 - 164: 5.630 distance: 163 - 164: 7.345 distance: 165 - 166: 6.399 distance: 166 - 169: 6.853 distance: 167 - 168: 6.292 distance: 167 - 172: 3.661 distance: 169 - 171: 5.537 distance: 172 - 173: 7.131 distance: 173 - 174: 8.872 distance: 174 - 175: 8.822 distance: 174 - 176: 11.663