Starting phenix.real_space_refine on Wed Mar 5 14:48:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j47_35972/03_2025/8j47_35972.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j47_35972/03_2025/8j47_35972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j47_35972/03_2025/8j47_35972.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j47_35972/03_2025/8j47_35972.map" model { file = "/net/cci-nas-00/data/ceres_data/8j47_35972/03_2025/8j47_35972.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j47_35972/03_2025/8j47_35972.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 10 5.16 5 C 1350 2.51 5 N 370 2.21 5 O 350 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2080 Number of models: 1 Model: "" Number of chains: 10 Chain: "D" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 208 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "C" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 208 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "F" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 208 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "E" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 208 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "B" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 208 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "A" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 208 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "H" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 208 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "G" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 208 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "J" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 208 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "I" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 208 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Time building chain proxies: 2.08, per 1000 atoms: 1.00 Number of scatterers: 2080 At special positions: 0 Unit cell: (72.908, 96.9345, 43.082, 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 10 16.00 O 350 8.00 N 370 7.00 C 1350 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.46 Conformation dependent library (CDL) restraints added in 260.9 milliseconds 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 460 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 31.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 16 through 20 removed outlier: 6.687A pdb=" N LYS D 16 " --> pdb=" O LEU F 17 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N PHE F 19 " --> pdb=" O LYS D 16 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL D 18 " --> pdb=" O PHE F 19 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LYS F 16 " --> pdb=" O LEU H 17 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N PHE H 19 " --> pdb=" O LYS F 16 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL F 18 " --> pdb=" O PHE H 19 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LYS H 16 " --> pdb=" O LEU J 17 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N PHE J 19 " --> pdb=" O LYS H 16 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL H 18 " --> pdb=" O PHE J 19 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 30 through 32 removed outlier: 6.250A pdb=" N ILE D 31 " --> pdb=" O ILE F 32 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ILE F 31 " --> pdb=" O ILE H 32 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE H 31 " --> pdb=" O ILE J 32 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 35 through 38 removed outlier: 6.241A pdb=" N VAL D 36 " --> pdb=" O GLY F 37 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL F 36 " --> pdb=" O GLY H 37 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL H 36 " --> pdb=" O GLY J 37 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 16 through 20 removed outlier: 6.617A pdb=" N LYS C 16 " --> pdb=" O LEU E 17 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N PHE E 19 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL C 18 " --> pdb=" O PHE E 19 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LYS E 16 " --> pdb=" O LEU G 17 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N PHE G 19 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL E 18 " --> pdb=" O PHE G 19 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LYS G 16 " --> pdb=" O LEU I 17 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N PHE I 19 " --> pdb=" O LYS G 16 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL G 18 " --> pdb=" O PHE I 19 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 30 through 32 removed outlier: 6.198A pdb=" N ILE C 31 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE E 31 " --> pdb=" O ILE G 32 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ILE G 31 " --> pdb=" O ILE I 32 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 35 through 38 removed outlier: 6.324A pdb=" N VAL C 36 " --> pdb=" O GLY E 37 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL E 36 " --> pdb=" O GLY G 37 " (cutoff:3.500A) 21 hydrogen bonds defined for protein. 63 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: 0.45 Time building geometry restraints manager: 0.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 680 1.34 - 1.46: 366 1.46 - 1.57: 1044 1.57 - 1.69: 0 1.69 - 1.80: 20 Bond restraints: 2110 Sorted by residual: bond pdb=" C ILE E 32 " pdb=" N GLY E 33 " ideal model delta sigma weight residual 1.335 1.326 0.010 1.19e-02 7.06e+03 6.43e-01 bond pdb=" CA VAL E 39 " pdb=" CB VAL E 39 " ideal model delta sigma weight residual 1.542 1.550 -0.008 1.08e-02 8.57e+03 5.74e-01 bond pdb=" C ILE A 32 " pdb=" N GLY A 33 " ideal model delta sigma weight residual 1.335 1.326 0.009 1.19e-02 7.06e+03 5.70e-01 bond pdb=" C ILE I 32 " pdb=" N GLY I 33 " ideal model delta sigma weight residual 1.335 1.326 0.009 1.19e-02 7.06e+03 5.55e-01 bond pdb=" C ILE G 32 " pdb=" N GLY G 33 " ideal model delta sigma weight residual 1.335 1.326 0.009 1.19e-02 7.06e+03 5.51e-01 ... (remaining 2105 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 2712 1.35 - 2.69: 72 2.69 - 4.04: 31 4.04 - 5.39: 10 5.39 - 6.73: 5 Bond angle restraints: 2830 Sorted by residual: angle pdb=" N VAL G 39 " pdb=" CA VAL G 39 " pdb=" C VAL G 39 " ideal model delta sigma weight residual 112.43 105.70 6.73 9.20e-01 1.18e+00 5.36e+01 angle pdb=" N VAL C 39 " pdb=" CA VAL C 39 " pdb=" C VAL C 39 " ideal model delta sigma weight residual 112.43 105.70 6.73 9.20e-01 1.18e+00 5.35e+01 angle pdb=" N VAL A 39 " pdb=" CA VAL A 39 " pdb=" C VAL A 39 " ideal model delta sigma weight residual 112.43 105.70 6.73 9.20e-01 1.18e+00 5.35e+01 angle pdb=" N VAL E 39 " pdb=" CA VAL E 39 " pdb=" C VAL E 39 " ideal model delta sigma weight residual 112.43 105.72 6.71 9.20e-01 1.18e+00 5.32e+01 angle pdb=" N VAL I 39 " pdb=" CA VAL I 39 " pdb=" C VAL I 39 " ideal model delta sigma weight residual 112.43 105.72 6.71 9.20e-01 1.18e+00 5.32e+01 ... (remaining 2825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.13: 989 16.13 - 32.27: 96 32.27 - 48.40: 60 48.40 - 64.53: 10 64.53 - 80.66: 5 Dihedral angle restraints: 1160 sinusoidal: 420 harmonic: 740 Sorted by residual: dihedral pdb=" CB LYS C 28 " pdb=" CG LYS C 28 " pdb=" CD LYS C 28 " pdb=" CE LYS C 28 " ideal model delta sinusoidal sigma weight residual -60.00 -118.75 58.75 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CB LYS G 28 " pdb=" CG LYS G 28 " pdb=" CD LYS G 28 " pdb=" CE LYS G 28 " ideal model delta sinusoidal sigma weight residual -60.00 -118.75 58.75 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CB LYS A 28 " pdb=" CG LYS A 28 " pdb=" CD LYS A 28 " pdb=" CE LYS A 28 " ideal model delta sinusoidal sigma weight residual -60.00 -118.75 58.75 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 1157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 127 0.026 - 0.052: 118 0.052 - 0.078: 20 0.078 - 0.104: 8 0.104 - 0.130: 57 Chirality restraints: 330 Sorted by residual: chirality pdb=" CA VAL E 39 " pdb=" N VAL E 39 " pdb=" C VAL E 39 " pdb=" CB VAL E 39 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA VAL C 39 " pdb=" N VAL C 39 " pdb=" C VAL C 39 " pdb=" CB VAL C 39 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CA VAL A 39 " pdb=" N VAL A 39 " pdb=" C VAL A 39 " pdb=" CB VAL A 39 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.20e-01 ... (remaining 327 not shown) Planarity restraints: 360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL E 39 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.71e+00 pdb=" C VAL E 39 " -0.028 2.00e-02 2.50e+03 pdb=" O VAL E 39 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL E 40 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 39 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.70e+00 pdb=" C VAL C 39 " -0.028 2.00e-02 2.50e+03 pdb=" O VAL C 39 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL C 40 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL G 39 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.67e+00 pdb=" C VAL G 39 " -0.028 2.00e-02 2.50e+03 pdb=" O VAL G 39 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL G 40 " 0.009 2.00e-02 2.50e+03 ... (remaining 357 not shown) Histogram of nonbonded interaction distances: 2.52 - 2.99: 1094 2.99 - 3.47: 1676 3.47 - 3.95: 3313 3.95 - 4.42: 3216 4.42 - 4.90: 6634 Nonbonded interactions: 15933 Sorted by model distance: nonbonded pdb=" N VAL A 39 " pdb=" N VAL A 40 " model vdw 2.518 2.560 nonbonded pdb=" N VAL G 39 " pdb=" N VAL G 40 " model vdw 2.518 2.560 nonbonded pdb=" N VAL C 39 " pdb=" N VAL C 40 " model vdw 2.518 2.560 nonbonded pdb=" N VAL E 39 " pdb=" N VAL E 40 " model vdw 2.519 2.560 nonbonded pdb=" N VAL I 39 " pdb=" N VAL I 40 " model vdw 2.519 2.560 ... (remaining 15928 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 10.600 Find NCS groups from input model: 0.090 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:13.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2110 Z= 0.279 Angle : 0.737 6.733 2830 Z= 0.501 Chirality : 0.057 0.130 330 Planarity : 0.003 0.016 360 Dihedral : 18.268 80.665 700 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 2.38 % Allowed : 30.95 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.51 (0.49), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS G 13 PHE 0.013 0.003 PHE E 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.211 Fit side-chains REVERT: D 23 ASP cc_start: 0.7156 (m-30) cc_final: 0.6747 (m-30) REVERT: C 15 GLN cc_start: 0.7463 (pp30) cc_final: 0.7243 (tt0) REVERT: C 23 ASP cc_start: 0.7337 (m-30) cc_final: 0.7133 (m-30) REVERT: F 23 ASP cc_start: 0.7125 (m-30) cc_final: 0.6693 (m-30) REVERT: E 15 GLN cc_start: 0.7541 (pp30) cc_final: 0.7255 (tt0) REVERT: E 26 SER cc_start: 0.8320 (p) cc_final: 0.8018 (p) REVERT: B 23 ASP cc_start: 0.7459 (m-30) cc_final: 0.7233 (m-30) REVERT: A 15 GLN cc_start: 0.7582 (pp30) cc_final: 0.7363 (tm-30) REVERT: A 23 ASP cc_start: 0.7520 (m-30) cc_final: 0.7262 (m-30) REVERT: A 34 LEU cc_start: 0.8117 (tt) cc_final: 0.7744 (tt) REVERT: J 35 MET cc_start: 0.7580 (ttp) cc_final: 0.7373 (ttm) REVERT: I 40 VAL cc_start: 0.7027 (OUTLIER) cc_final: 0.6776 (p) outliers start: 5 outliers final: 3 residues processed: 62 average time/residue: 0.8550 time to fit residues: 54.3771 Evaluate side-chains 55 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain I residue 40 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 15 GLN I 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.152764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.101046 restraints weight = 1784.864| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.31 r_work: 0.3234 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 2110 Z= 0.453 Angle : 0.873 8.558 2830 Z= 0.419 Chirality : 0.066 0.177 330 Planarity : 0.004 0.020 360 Dihedral : 8.164 51.098 294 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 13.33 % Allowed : 19.05 % Favored : 67.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.86 (0.45), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 13 PHE 0.022 0.004 PHE J 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 61 time to evaluate : 0.211 Fit side-chains REVERT: C 13 HIS cc_start: 0.4249 (OUTLIER) cc_final: 0.3977 (m-70) REVERT: C 15 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7337 (tt0) REVERT: E 13 HIS cc_start: 0.4198 (OUTLIER) cc_final: 0.3934 (m-70) REVERT: E 15 GLN cc_start: 0.7656 (OUTLIER) cc_final: 0.7286 (tt0) REVERT: E 26 SER cc_start: 0.8698 (p) cc_final: 0.8470 (p) REVERT: A 13 HIS cc_start: 0.4657 (OUTLIER) cc_final: 0.4218 (m90) REVERT: A 15 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7477 (tt0) REVERT: A 34 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8396 (mp) REVERT: H 23 ASP cc_start: 0.7878 (m-30) cc_final: 0.7644 (m-30) REVERT: G 13 HIS cc_start: 0.4304 (OUTLIER) cc_final: 0.3831 (m-70) REVERT: I 13 HIS cc_start: 0.4743 (OUTLIER) cc_final: 0.4407 (m170) REVERT: I 16 LYS cc_start: 0.7799 (ttpt) cc_final: 0.7343 (ptmm) REVERT: I 17 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7639 (pp) outliers start: 28 outliers final: 12 residues processed: 71 average time/residue: 0.7295 time to fit residues: 53.3491 Evaluate side-chains 77 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 55 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain C residue 13 HIS Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 26 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 5 optimal weight: 8.9990 chunk 8 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 1 optimal weight: 0.7980 chunk 15 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 18 optimal weight: 0.7980 chunk 2 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.154352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.101834 restraints weight = 1751.981| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.33 r_work: 0.3257 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 2110 Z= 0.337 Angle : 0.766 7.716 2830 Z= 0.359 Chirality : 0.060 0.135 330 Planarity : 0.003 0.015 360 Dihedral : 7.847 43.461 293 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.74 % Favored : 89.26 % Rotamer: Outliers : 14.29 % Allowed : 15.71 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.03 (0.43), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.30 (0.33), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 14 PHE 0.017 0.003 PHE C 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 56 time to evaluate : 0.235 Fit side-chains REVERT: D 13 HIS cc_start: 0.4717 (OUTLIER) cc_final: 0.4311 (m-70) REVERT: C 13 HIS cc_start: 0.4237 (OUTLIER) cc_final: 0.3989 (m-70) REVERT: C 15 GLN cc_start: 0.7738 (OUTLIER) cc_final: 0.7280 (tt0) REVERT: E 15 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.7258 (tt0) REVERT: E 26 SER cc_start: 0.8796 (p) cc_final: 0.8572 (p) REVERT: B 13 HIS cc_start: 0.5058 (OUTLIER) cc_final: 0.4126 (t70) REVERT: A 13 HIS cc_start: 0.4714 (OUTLIER) cc_final: 0.4309 (m-70) REVERT: A 15 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.7475 (OUTLIER) REVERT: A 34 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8356 (mp) REVERT: H 23 ASP cc_start: 0.7864 (m-30) cc_final: 0.7659 (m-30) REVERT: J 13 HIS cc_start: 0.5029 (OUTLIER) cc_final: 0.4817 (m-70) REVERT: I 17 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7533 (pp) outliers start: 30 outliers final: 14 residues processed: 70 average time/residue: 0.6440 time to fit residues: 46.6368 Evaluate side-chains 78 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 55 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain C residue 13 HIS Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain J residue 13 HIS Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 26 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 6 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 16 optimal weight: 0.0370 chunk 8 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 overall best weight: 4.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.153098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.101011 restraints weight = 1755.469| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.28 r_work: 0.3253 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 2110 Z= 0.420 Angle : 0.846 9.324 2830 Z= 0.384 Chirality : 0.063 0.150 330 Planarity : 0.003 0.020 360 Dihedral : 8.426 48.334 293 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 14.29 % Allowed : 14.76 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.22 (0.42), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.32), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS D 14 PHE 0.020 0.003 PHE J 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 55 time to evaluate : 0.232 Fit side-chains REVERT: D 13 HIS cc_start: 0.4658 (OUTLIER) cc_final: 0.4222 (m-70) REVERT: C 13 HIS cc_start: 0.4450 (OUTLIER) cc_final: 0.3948 (m-70) REVERT: E 13 HIS cc_start: 0.4331 (OUTLIER) cc_final: 0.4056 (m170) REVERT: E 15 GLN cc_start: 0.7516 (OUTLIER) cc_final: 0.7044 (tt0) REVERT: E 26 SER cc_start: 0.8710 (p) cc_final: 0.8496 (p) REVERT: B 13 HIS cc_start: 0.5085 (OUTLIER) cc_final: 0.4196 (t70) REVERT: A 13 HIS cc_start: 0.4730 (OUTLIER) cc_final: 0.4350 (m-70) REVERT: A 15 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.7487 (OUTLIER) REVERT: A 34 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8331 (mp) REVERT: J 13 HIS cc_start: 0.5124 (OUTLIER) cc_final: 0.4875 (m-70) REVERT: I 17 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7564 (pp) outliers start: 30 outliers final: 18 residues processed: 69 average time/residue: 0.8035 time to fit residues: 57.1618 Evaluate side-chains 81 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 54 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain C residue 13 HIS Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain F residue 15 GLN Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain J residue 13 HIS Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 26 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 0.5980 chunk 4 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 5 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.155107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.102732 restraints weight = 1749.029| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.31 r_work: 0.3268 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2110 Z= 0.208 Angle : 0.644 7.318 2830 Z= 0.298 Chirality : 0.055 0.128 330 Planarity : 0.002 0.012 360 Dihedral : 7.384 40.732 293 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 15.24 % Allowed : 18.57 % Favored : 66.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.17 (0.42), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.32), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 14 PHE 0.011 0.002 PHE J 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 60 time to evaluate : 0.211 Fit side-chains REVERT: D 13 HIS cc_start: 0.4381 (OUTLIER) cc_final: 0.3993 (m-70) REVERT: C 13 HIS cc_start: 0.4159 (OUTLIER) cc_final: 0.3685 (m90) REVERT: E 26 SER cc_start: 0.8781 (p) cc_final: 0.8560 (p) REVERT: A 13 HIS cc_start: 0.4618 (OUTLIER) cc_final: 0.4369 (m-70) REVERT: A 15 GLN cc_start: 0.7716 (OUTLIER) cc_final: 0.7481 (tt0) REVERT: A 34 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8335 (mp) REVERT: J 13 HIS cc_start: 0.5089 (OUTLIER) cc_final: 0.4863 (m-70) REVERT: I 17 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7458 (pp) outliers start: 32 outliers final: 18 residues processed: 73 average time/residue: 0.7073 time to fit residues: 53.2266 Evaluate side-chains 81 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 56 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain C residue 13 HIS Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain F residue 15 GLN Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain J residue 13 HIS Chi-restraints excluded: chain J residue 15 GLN Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 26 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 15 optimal weight: 0.1980 chunk 9 optimal weight: 5.9990 overall best weight: 4.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.153622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.101299 restraints weight = 1758.417| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.30 r_work: 0.3252 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 2110 Z= 0.439 Angle : 0.853 11.148 2830 Z= 0.387 Chirality : 0.063 0.150 330 Planarity : 0.003 0.017 360 Dihedral : 8.297 50.342 293 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 14.76 % Allowed : 18.10 % Favored : 67.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.32 (0.42), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.32), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 14 PHE 0.020 0.003 PHE J 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 55 time to evaluate : 0.214 Fit side-chains REVERT: D 13 HIS cc_start: 0.4433 (OUTLIER) cc_final: 0.4085 (m-70) REVERT: C 13 HIS cc_start: 0.4289 (OUTLIER) cc_final: 0.3701 (m90) REVERT: E 13 HIS cc_start: 0.4450 (OUTLIER) cc_final: 0.4112 (m170) REVERT: E 26 SER cc_start: 0.8771 (p) cc_final: 0.8563 (p) REVERT: B 13 HIS cc_start: 0.5082 (OUTLIER) cc_final: 0.4210 (t70) REVERT: A 13 HIS cc_start: 0.4780 (OUTLIER) cc_final: 0.4423 (m-70) REVERT: A 34 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8358 (mp) REVERT: I 17 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7554 (pp) outliers start: 31 outliers final: 18 residues processed: 70 average time/residue: 0.6711 time to fit residues: 48.6038 Evaluate side-chains 78 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 53 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain C residue 13 HIS Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain J residue 15 GLN Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 26 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 15 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 15 GLN A 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.153268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.103154 restraints weight = 1851.252| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.26 r_work: 0.3262 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 2110 Z= 0.380 Angle : 0.818 11.030 2830 Z= 0.370 Chirality : 0.061 0.139 330 Planarity : 0.003 0.016 360 Dihedral : 8.140 49.918 293 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 14.76 % Allowed : 18.57 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.41), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.31), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 14 PHE 0.017 0.003 PHE J 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 55 time to evaluate : 0.253 Fit side-chains REVERT: D 13 HIS cc_start: 0.4407 (OUTLIER) cc_final: 0.4062 (m-70) REVERT: C 13 HIS cc_start: 0.4300 (OUTLIER) cc_final: 0.3792 (m90) REVERT: E 13 HIS cc_start: 0.4637 (OUTLIER) cc_final: 0.4334 (m90) REVERT: B 13 HIS cc_start: 0.5084 (OUTLIER) cc_final: 0.4188 (t70) REVERT: A 13 HIS cc_start: 0.4769 (OUTLIER) cc_final: 0.4419 (m-70) REVERT: A 15 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.7302 (tt0) REVERT: A 34 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8342 (mp) REVERT: I 17 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7543 (pp) outliers start: 31 outliers final: 20 residues processed: 70 average time/residue: 0.6795 time to fit residues: 49.1259 Evaluate side-chains 81 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 53 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain C residue 13 HIS Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain F residue 15 GLN Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain J residue 15 GLN Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 26 SER 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: 52.4267 > 50: distance: 90 - 98: 3.343 distance: 98 - 99: 3.059 distance: 99 - 100: 6.906 distance: 99 - 102: 9.891 distance: 100 - 101: 13.255 distance: 100 - 103: 10.462 distance: 103 - 104: 13.103 distance: 104 - 105: 16.039 distance: 105 - 106: 21.152 distance: 105 - 107: 10.476 distance: 107 - 108: 5.752 distance: 108 - 109: 7.086 distance: 108 - 111: 3.391 distance: 109 - 110: 6.258 distance: 109 - 115: 3.921 distance: 111 - 112: 4.409 distance: 112 - 113: 6.122 distance: 112 - 114: 3.226 distance: 116 - 117: 5.170 distance: 116 - 119: 6.962 distance: 117 - 118: 16.574 distance: 117 - 122: 10.272 distance: 119 - 120: 4.958 distance: 119 - 121: 7.394 distance: 122 - 123: 6.568 distance: 123 - 124: 8.987 distance: 124 - 125: 13.054 distance: 124 - 126: 13.612 distance: 127 - 128: 9.168 distance: 127 - 130: 10.341 distance: 128 - 129: 4.458 distance: 128 - 132: 4.939 distance: 130 - 131: 8.756 distance: 132 - 133: 6.075 distance: 133 - 134: 4.521 distance: 134 - 135: 9.488 distance: 136 - 137: 7.526 distance: 137 - 138: 7.943 distance: 137 - 139: 8.370 distance: 141 - 142: 6.799 distance: 142 - 143: 4.514 distance: 142 - 149: 4.774 distance: 144 - 145: 8.140 distance: 145 - 146: 7.536 distance: 146 - 147: 12.195 distance: 147 - 148: 3.955 distance: 149 - 150: 7.864 distance: 150 - 151: 9.490 distance: 151 - 152: 3.267 distance: 151 - 153: 8.436 distance: 153 - 154: 8.943 distance: 154 - 155: 19.785 distance: 154 - 157: 16.464 distance: 155 - 156: 20.397 distance: 155 - 158: 17.562