Starting phenix.real_space_refine on Fri Aug 22 14:46:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dkm_27490/08_2025/8dkm_27490.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dkm_27490/08_2025/8dkm_27490.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dkm_27490/08_2025/8dkm_27490.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dkm_27490/08_2025/8dkm_27490.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dkm_27490/08_2025/8dkm_27490.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dkm_27490/08_2025/8dkm_27490.map" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.004 sd= 0.074 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 17 5.16 5 C 2867 2.51 5 N 706 2.21 5 O 793 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4383 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 876 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "B" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "P" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2679 Classifications: {'peptide': 334} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 15, 'TRANS': 318} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "P" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'IYY': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.28, per 1000 atoms: 0.29 Number of scatterers: 4383 At special positions: 0 Unit cell: (85.884, 105.25, 106.092, 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 17 16.00 O 793 8.00 N 706 7.00 C 2867 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " 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 Time building additional restraints: 0.43 Conformation dependent library (CDL) restraints added in 194.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1020 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 8 sheets defined 38.2% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 88 through 92 removed outlier: 3.936A pdb=" N THR A 92 " --> pdb=" O SER A 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.939A pdb=" N ILE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 120 through 141 removed outlier: 3.651A pdb=" N SER P 124 " --> pdb=" O SER P 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 141 through 150 removed outlier: 4.651A pdb=" N GLN P 145 " --> pdb=" O SER P 141 " (cutoff:3.500A) Processing helix chain 'P' and resid 159 through 179 Processing helix chain 'P' and resid 183 through 194 Processing helix chain 'P' and resid 202 through 226 Processing helix chain 'P' and resid 234 through 257 removed outlier: 3.620A pdb=" N VAL P 257 " --> pdb=" O ILE P 253 " (cutoff:3.500A) Processing helix chain 'P' and resid 261 through 279 removed outlier: 3.542A pdb=" N PHE P 265 " --> pdb=" O THR P 261 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE P 269 " --> pdb=" O PHE P 265 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER P 270 " --> pdb=" O LEU P 266 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL P 276 " --> pdb=" O ILE P 272 " (cutoff:3.500A) Processing helix chain 'P' and resid 281 through 292 Processing helix chain 'P' and resid 298 through 323 removed outlier: 3.725A pdb=" N VAL P 302 " --> pdb=" O SER P 298 " (cutoff:3.500A) Processing helix chain 'P' and resid 325 through 330 Processing helix chain 'P' and resid 332 through 355 removed outlier: 3.632A pdb=" N PHE P 336 " --> pdb=" O ASP P 332 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LEU P 338 " --> pdb=" O THR P 334 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 50 removed outlier: 6.628A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 5 through 6 removed outlier: 3.973A pdb=" N PHE B 71 " --> pdb=" O CYS B 23 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.420A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 45 through 48 removed outlier: 6.435A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 26 through 27 removed outlier: 3.595A pdb=" N THR P 90 " --> pdb=" O GLU P 71 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'P' and resid 31 through 35 removed outlier: 3.589A pdb=" N VAL P 32 " --> pdb=" O ARG P 114 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LEU P 101 " --> pdb=" O GLY P 110 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ARG P 112 " --> pdb=" O VAL P 99 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL P 99 " --> pdb=" O ARG P 112 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N THR P 98 " --> pdb=" O THR P 61 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR P 57 " --> pdb=" O HIS P 102 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'P' and resid 31 through 35 removed outlier: 3.589A pdb=" N VAL P 32 " --> pdb=" O ARG P 114 " (cutoff:3.500A) 222 hydrogen bonds defined for protein. 621 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: 0.65 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: 1.20 - 1.38: 1570 1.38 - 1.56: 2907 1.56 - 1.74: 0 1.74 - 1.92: 24 1.92 - 2.10: 1 Bond restraints: 4502 Sorted by residual: bond pdb=" C ASN P 301 " pdb=" O ASN P 301 " ideal model delta sigma weight residual 1.237 1.198 0.039 1.17e-02 7.31e+03 1.10e+01 bond pdb=" N ILE P 260 " pdb=" CA ILE P 260 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.18e-02 7.18e+03 9.88e+00 bond pdb=" N THR P 261 " pdb=" CA THR P 261 " ideal model delta sigma weight residual 1.452 1.488 -0.035 1.25e-02 6.40e+03 7.98e+00 bond pdb=" CA VAL P 302 " pdb=" CB VAL P 302 " ideal model delta sigma weight residual 1.540 1.501 0.038 1.37e-02 5.33e+03 7.81e+00 bond pdb=" N VAL P 259 " pdb=" CA VAL P 259 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.42e-02 4.96e+03 5.60e+00 ... (remaining 4497 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 5916 1.49 - 2.98: 158 2.98 - 4.48: 44 4.48 - 5.97: 12 5.97 - 7.46: 8 Bond angle restraints: 6138 Sorted by residual: angle pdb=" N GLY P 300 " pdb=" CA GLY P 300 " pdb=" C GLY P 300 " ideal model delta sigma weight residual 113.37 105.91 7.46 1.34e+00 5.57e-01 3.10e+01 angle pdb=" N TYR P 271 " pdb=" CA TYR P 271 " pdb=" C TYR P 271 " ideal model delta sigma weight residual 111.36 115.75 -4.39 1.09e+00 8.42e-01 1.62e+01 angle pdb=" N VAL P 259 " pdb=" CA VAL P 259 " pdb=" C VAL P 259 " ideal model delta sigma weight residual 111.45 107.73 3.72 9.30e-01 1.16e+00 1.60e+01 angle pdb=" C PRO A 62 " pdb=" N ASP A 63 " pdb=" CA ASP A 63 " ideal model delta sigma weight residual 121.54 128.03 -6.49 1.91e+00 2.74e-01 1.16e+01 angle pdb=" CA THR P 261 " pdb=" C THR P 261 " pdb=" O THR P 261 " ideal model delta sigma weight residual 121.82 118.01 3.81 1.21e+00 6.83e-01 9.94e+00 ... (remaining 6133 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.19: 2277 15.19 - 30.38: 250 30.38 - 45.57: 53 45.57 - 60.76: 8 60.76 - 75.94: 8 Dihedral angle restraints: 2596 sinusoidal: 999 harmonic: 1597 Sorted by residual: dihedral pdb=" CA SER P 270 " pdb=" C SER P 270 " pdb=" N TYR P 271 " pdb=" CA TYR P 271 " ideal model delta harmonic sigma weight residual 180.00 157.07 22.93 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CB CYS B 23 " pdb=" SG CYS B 23 " pdb=" SG CYS B 88 " pdb=" CB CYS B 88 " ideal model delta sinusoidal sigma weight residual 93.00 61.96 31.04 1 1.00e+01 1.00e-02 1.37e+01 dihedral pdb=" CA ARG P 47 " pdb=" C ARG P 47 " pdb=" N PRO P 48 " pdb=" CA PRO P 48 " ideal model delta harmonic sigma weight residual 180.00 163.67 16.33 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 2593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 549 0.050 - 0.100: 116 0.100 - 0.150: 26 0.150 - 0.200: 3 0.200 - 0.250: 1 Chirality restraints: 695 Sorted by residual: chirality pdb=" CA TYR P 271 " pdb=" N TYR P 271 " pdb=" C TYR P 271 " pdb=" CB TYR P 271 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA VAL P 259 " pdb=" N VAL P 259 " pdb=" C VAL P 259 " pdb=" CB VAL P 259 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.39e-01 chirality pdb=" CB VAL P 279 " pdb=" CA VAL P 279 " pdb=" CG1 VAL P 279 " pdb=" CG2 VAL P 279 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.88e-01 ... (remaining 692 not shown) Planarity restraints: 767 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN P 199 " 0.045 5.00e-02 4.00e+02 6.80e-02 7.39e+00 pdb=" N PRO P 200 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO P 200 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO P 200 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP P 182 " -0.014 2.00e-02 2.50e+03 1.10e-02 3.02e+00 pdb=" CG TRP P 182 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP P 182 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP P 182 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP P 182 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP P 182 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP P 182 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP P 182 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP P 182 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP P 182 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP P 235 " 0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO P 236 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO P 236 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO P 236 " 0.021 5.00e-02 4.00e+02 ... (remaining 764 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 797 2.77 - 3.30: 4104 3.30 - 3.84: 7025 3.84 - 4.37: 7958 4.37 - 4.90: 14353 Nonbonded interactions: 34237 Sorted by model distance: nonbonded pdb=" O SER A 52 " pdb=" NH1 ARG A 73 " model vdw 2.241 3.120 nonbonded pdb=" OG1 THR A 40 " pdb=" O GLU A 42 " model vdw 2.245 3.040 nonbonded pdb=" O PHE A 29 " pdb=" NH2 ARG A 73 " model vdw 2.265 3.120 nonbonded pdb=" OD1 ASP B 42 " pdb=" N ILE B 43 " model vdw 2.277 3.120 nonbonded pdb=" OD1 ASP P 161 " pdb=" N PHE P 162 " model vdw 2.285 3.120 ... (remaining 34232 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=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: 2.310 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.200 Find NCS groups from input model: 0.020 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: 0.000 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 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 : 0.003 0.039 4504 Z= 0.196 Angle : 0.673 7.461 6142 Z= 0.357 Chirality : 0.045 0.250 695 Planarity : 0.005 0.068 767 Dihedral : 13.474 75.945 1570 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 0.83 % Allowed : 0.41 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.37), residues: 547 helix: 1.16 (0.39), residues: 198 sheet: -0.77 (0.48), residues: 131 loop : -2.24 (0.39), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 24 TYR 0.015 0.001 TYR P 286 PHE 0.017 0.001 PHE P 289 TRP 0.030 0.001 TRP P 182 HIS 0.002 0.001 HIS P 211 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 4502) covalent geometry : angle 0.67308 ( 6138) SS BOND : bond 0.00256 ( 2) SS BOND : angle 1.03537 ( 4) hydrogen bonds : bond 0.14622 ( 219) hydrogen bonds : angle 6.33353 ( 621) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.174 Fit side-chains REVERT: A 83 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7269 (tp-100) REVERT: B 81 GLU cc_start: 0.7038 (mp0) cc_final: 0.6829 (mp0) outliers start: 4 outliers final: 2 residues processed: 83 average time/residue: 0.0651 time to fit residues: 7.1825 Evaluate side-chains 70 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain P residue 260 ILE Chi-restraints excluded: chain P residue 272 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN P 149 ASN P 301 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.151919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.121723 restraints weight = 5563.408| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.18 r_work: 0.3137 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4504 Z= 0.166 Angle : 0.609 7.674 6142 Z= 0.311 Chirality : 0.044 0.153 695 Planarity : 0.005 0.043 767 Dihedral : 6.341 66.872 618 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.11 % Allowed : 9.34 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.38), residues: 547 helix: 1.47 (0.38), residues: 199 sheet: -0.76 (0.49), residues: 133 loop : -2.04 (0.41), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 24 TYR 0.022 0.002 TYR P 134 PHE 0.021 0.001 PHE P 289 TRP 0.024 0.001 TRP P 182 HIS 0.003 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 4502) covalent geometry : angle 0.60841 ( 6138) SS BOND : bond 0.00690 ( 2) SS BOND : angle 1.26563 ( 4) hydrogen bonds : bond 0.04070 ( 219) hydrogen bonds : angle 4.72182 ( 621) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.169 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: P 148 MET cc_start: 0.8637 (tmm) cc_final: 0.8203 (tmm) REVERT: P 287 MET cc_start: 0.7940 (ttm) cc_final: 0.7478 (ttp) REVERT: P 290 TYR cc_start: 0.7743 (t80) cc_final: 0.7537 (t80) outliers start: 15 outliers final: 14 residues processed: 82 average time/residue: 0.0553 time to fit residues: 6.2517 Evaluate side-chains 86 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 149 ASN Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 198 VAL Chi-restraints excluded: chain P residue 252 MET Chi-restraints excluded: chain P residue 260 ILE Chi-restraints excluded: chain P residue 347 VAL Chi-restraints excluded: chain P residue 348 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 51 optimal weight: 0.0980 chunk 47 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 38 optimal weight: 0.0020 chunk 0 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN ** P 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.153901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.124064 restraints weight = 5552.662| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.17 r_work: 0.3193 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4504 Z= 0.117 Angle : 0.555 6.934 6142 Z= 0.283 Chirality : 0.042 0.146 695 Planarity : 0.004 0.036 767 Dihedral : 5.953 65.078 616 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.28 % Allowed : 13.90 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.37), residues: 547 helix: 1.51 (0.37), residues: 205 sheet: -0.57 (0.49), residues: 131 loop : -1.99 (0.42), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 24 TYR 0.018 0.001 TYR P 134 PHE 0.010 0.001 PHE P 345 TRP 0.015 0.001 TRP P 182 HIS 0.001 0.000 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 4502) covalent geometry : angle 0.55466 ( 6138) SS BOND : bond 0.00375 ( 2) SS BOND : angle 0.93239 ( 4) hydrogen bonds : bond 0.03434 ( 219) hydrogen bonds : angle 4.37435 ( 621) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.203 Fit side-chains REVERT: B 61 ARG cc_start: 0.7756 (mtp180) cc_final: 0.7534 (mtp180) outliers start: 11 outliers final: 10 residues processed: 78 average time/residue: 0.0648 time to fit residues: 6.7974 Evaluate side-chains 81 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 198 VAL Chi-restraints excluded: chain P residue 252 MET Chi-restraints excluded: chain P residue 260 ILE Chi-restraints excluded: chain P residue 348 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 4 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN ** P 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.149625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.119864 restraints weight = 5537.425| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.14 r_work: 0.3135 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 4504 Z= 0.189 Angle : 0.607 7.757 6142 Z= 0.312 Chirality : 0.045 0.160 695 Planarity : 0.005 0.034 767 Dihedral : 6.103 62.774 616 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 4.15 % Allowed : 13.28 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.38), residues: 547 helix: 1.88 (0.38), residues: 199 sheet: -0.71 (0.49), residues: 133 loop : -1.99 (0.42), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 24 TYR 0.020 0.002 TYR P 134 PHE 0.024 0.001 PHE P 289 TRP 0.018 0.002 TRP P 182 HIS 0.003 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 4502) covalent geometry : angle 0.60600 ( 6138) SS BOND : bond 0.00495 ( 2) SS BOND : angle 1.17521 ( 4) hydrogen bonds : bond 0.03992 ( 219) hydrogen bonds : angle 4.45919 ( 621) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.197 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: B 61 ARG cc_start: 0.7797 (mtp180) cc_final: 0.7494 (mtp180) REVERT: P 287 MET cc_start: 0.8103 (ttp) cc_final: 0.7237 (ttt) outliers start: 20 outliers final: 16 residues processed: 83 average time/residue: 0.0625 time to fit residues: 6.9802 Evaluate side-chains 86 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 198 VAL Chi-restraints excluded: chain P residue 252 MET Chi-restraints excluded: chain P residue 260 ILE Chi-restraints excluded: chain P residue 344 VAL Chi-restraints excluded: chain P residue 347 VAL Chi-restraints excluded: chain P residue 348 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 41 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 5 optimal weight: 0.0770 chunk 17 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 38 GLN ** P 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.151988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.122503 restraints weight = 5617.630| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.14 r_work: 0.3149 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4504 Z= 0.133 Angle : 0.573 7.186 6142 Z= 0.294 Chirality : 0.043 0.147 695 Planarity : 0.004 0.033 767 Dihedral : 5.944 61.573 616 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.22 % Favored : 93.60 % Rotamer: Outliers : 3.32 % Allowed : 15.35 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.38), residues: 547 helix: 1.94 (0.38), residues: 199 sheet: -0.90 (0.48), residues: 141 loop : -1.90 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 24 TYR 0.017 0.001 TYR P 134 PHE 0.010 0.001 PHE P 345 TRP 0.013 0.001 TRP B 32 HIS 0.001 0.000 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 4502) covalent geometry : angle 0.57306 ( 6138) SS BOND : bond 0.00399 ( 2) SS BOND : angle 0.71106 ( 4) hydrogen bonds : bond 0.03428 ( 219) hydrogen bonds : angle 4.24926 ( 621) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.171 Fit side-chains REVERT: A 83 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.7537 (tp-100) outliers start: 16 outliers final: 13 residues processed: 78 average time/residue: 0.0639 time to fit residues: 6.6905 Evaluate side-chains 84 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 198 VAL Chi-restraints excluded: chain P residue 252 MET Chi-restraints excluded: chain P residue 260 ILE Chi-restraints excluded: chain P residue 347 VAL Chi-restraints excluded: chain P residue 348 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 4.9990 chunk 21 optimal weight: 0.0670 chunk 30 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 38 GLN P 222 GLN ** P 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 301 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.152707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.122819 restraints weight = 5685.710| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.18 r_work: 0.3153 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4504 Z= 0.129 Angle : 0.566 6.986 6142 Z= 0.290 Chirality : 0.043 0.147 695 Planarity : 0.004 0.032 767 Dihedral : 5.865 59.648 616 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.48 % Favored : 94.33 % Rotamer: Outliers : 3.73 % Allowed : 15.15 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.39), residues: 547 helix: 2.04 (0.38), residues: 198 sheet: -0.89 (0.48), residues: 141 loop : -1.83 (0.43), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 24 TYR 0.018 0.001 TYR P 134 PHE 0.011 0.001 PHE P 345 TRP 0.010 0.001 TRP P 182 HIS 0.002 0.000 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 4502) covalent geometry : angle 0.56293 ( 6138) SS BOND : bond 0.00400 ( 2) SS BOND : angle 2.49957 ( 4) hydrogen bonds : bond 0.03346 ( 219) hydrogen bonds : angle 4.15683 ( 621) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.166 Fit side-chains REVERT: A 18 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8497 (tt) REVERT: A 83 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.7551 (tp-100) REVERT: P 148 MET cc_start: 0.8470 (tmm) cc_final: 0.8184 (tmm) outliers start: 18 outliers final: 13 residues processed: 78 average time/residue: 0.0562 time to fit residues: 6.0531 Evaluate side-chains 83 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 198 VAL Chi-restraints excluded: chain P residue 252 MET Chi-restraints excluded: chain P residue 260 ILE Chi-restraints excluded: chain P residue 347 VAL Chi-restraints excluded: chain P residue 348 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 13 optimal weight: 3.9990 chunk 18 optimal weight: 0.0050 chunk 35 optimal weight: 0.6980 chunk 51 optimal weight: 0.2980 chunk 12 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 GLN ** P 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.153604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.123288 restraints weight = 5569.413| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.20 r_work: 0.3141 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4504 Z= 0.125 Angle : 0.558 6.811 6142 Z= 0.286 Chirality : 0.043 0.146 695 Planarity : 0.004 0.032 767 Dihedral : 5.799 58.470 616 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.85 % Favored : 93.97 % Rotamer: Outliers : 3.73 % Allowed : 15.56 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.39), residues: 547 helix: 1.85 (0.38), residues: 205 sheet: -0.77 (0.48), residues: 139 loop : -1.80 (0.44), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 24 TYR 0.017 0.001 TYR P 134 PHE 0.011 0.001 PHE P 345 TRP 0.009 0.001 TRP P 132 HIS 0.001 0.000 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 4502) covalent geometry : angle 0.55449 ( 6138) SS BOND : bond 0.00380 ( 2) SS BOND : angle 2.55449 ( 4) hydrogen bonds : bond 0.03250 ( 219) hydrogen bonds : angle 4.08947 ( 621) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.194 Fit side-chains REVERT: A 18 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8483 (tt) REVERT: A 83 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.7549 (tp-100) outliers start: 18 outliers final: 15 residues processed: 75 average time/residue: 0.0547 time to fit residues: 5.7617 Evaluate side-chains 84 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 198 VAL Chi-restraints excluded: chain P residue 252 MET Chi-restraints excluded: chain P residue 260 ILE Chi-restraints excluded: chain P residue 344 VAL Chi-restraints excluded: chain P residue 347 VAL Chi-restraints excluded: chain P residue 348 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 38 GLN ** P 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.151949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.122157 restraints weight = 5561.034| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.14 r_work: 0.3128 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4504 Z= 0.145 Angle : 0.569 7.013 6142 Z= 0.292 Chirality : 0.043 0.150 695 Planarity : 0.004 0.036 767 Dihedral : 5.860 57.987 616 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.03 % Favored : 93.78 % Rotamer: Outliers : 4.15 % Allowed : 15.98 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.39), residues: 547 helix: 1.99 (0.38), residues: 200 sheet: -0.81 (0.47), residues: 146 loop : -1.69 (0.45), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 24 TYR 0.018 0.001 TYR P 134 PHE 0.011 0.001 PHE P 87 TRP 0.010 0.001 TRP P 132 HIS 0.002 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 4502) covalent geometry : angle 0.56602 ( 6138) SS BOND : bond 0.00485 ( 2) SS BOND : angle 2.45657 ( 4) hydrogen bonds : bond 0.03464 ( 219) hydrogen bonds : angle 4.17753 ( 621) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.175 Fit side-chains REVERT: A 18 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8530 (tt) REVERT: A 83 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.7596 (tp-100) REVERT: P 286 TYR cc_start: 0.7611 (t80) cc_final: 0.7411 (t80) outliers start: 20 outliers final: 17 residues processed: 75 average time/residue: 0.0525 time to fit residues: 5.5330 Evaluate side-chains 86 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 198 VAL Chi-restraints excluded: chain P residue 217 LEU Chi-restraints excluded: chain P residue 252 MET Chi-restraints excluded: chain P residue 260 ILE Chi-restraints excluded: chain P residue 344 VAL Chi-restraints excluded: chain P residue 347 VAL Chi-restraints excluded: chain P residue 348 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 51 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 26 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 0.0870 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 38 GLN P 222 GLN ** P 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.153013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.122654 restraints weight = 5612.041| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.19 r_work: 0.3134 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4504 Z= 0.134 Angle : 0.572 6.941 6142 Z= 0.292 Chirality : 0.043 0.148 695 Planarity : 0.004 0.036 767 Dihedral : 5.827 57.476 616 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.67 % Favored : 94.15 % Rotamer: Outliers : 3.73 % Allowed : 16.18 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.39), residues: 547 helix: 2.01 (0.38), residues: 200 sheet: -0.77 (0.47), residues: 146 loop : -1.65 (0.45), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 24 TYR 0.017 0.001 TYR P 134 PHE 0.011 0.001 PHE P 345 TRP 0.009 0.001 TRP P 132 HIS 0.001 0.000 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 4502) covalent geometry : angle 0.56950 ( 6138) SS BOND : bond 0.00411 ( 2) SS BOND : angle 2.25180 ( 4) hydrogen bonds : bond 0.03354 ( 219) hydrogen bonds : angle 4.14269 ( 621) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.262 Fit side-chains REVERT: A 18 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8508 (tt) REVERT: A 83 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.7591 (tp-100) outliers start: 18 outliers final: 16 residues processed: 74 average time/residue: 0.0561 time to fit residues: 5.8365 Evaluate side-chains 86 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 198 VAL Chi-restraints excluded: chain P residue 217 LEU Chi-restraints excluded: chain P residue 252 MET Chi-restraints excluded: chain P residue 260 ILE Chi-restraints excluded: chain P residue 344 VAL Chi-restraints excluded: chain P residue 347 VAL Chi-restraints excluded: chain P residue 348 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 GLN ** P 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.151464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.121502 restraints weight = 5578.542| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.14 r_work: 0.3122 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4504 Z= 0.149 Angle : 0.580 7.140 6142 Z= 0.297 Chirality : 0.043 0.150 695 Planarity : 0.004 0.038 767 Dihedral : 5.893 57.211 616 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.03 % Favored : 93.78 % Rotamer: Outliers : 3.73 % Allowed : 16.60 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.39), residues: 547 helix: 1.99 (0.38), residues: 200 sheet: -0.78 (0.47), residues: 146 loop : -1.68 (0.45), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 24 TYR 0.018 0.001 TYR P 134 PHE 0.011 0.001 PHE P 87 TRP 0.010 0.001 TRP P 182 HIS 0.002 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 4502) covalent geometry : angle 0.57763 ( 6138) SS BOND : bond 0.00435 ( 2) SS BOND : angle 2.28704 ( 4) hydrogen bonds : bond 0.03524 ( 219) hydrogen bonds : angle 4.18912 ( 621) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.172 Fit side-chains REVERT: A 18 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8603 (tt) REVERT: A 83 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.7696 (tp-100) REVERT: P 286 TYR cc_start: 0.7562 (t80) cc_final: 0.7342 (t80) outliers start: 18 outliers final: 16 residues processed: 75 average time/residue: 0.0533 time to fit residues: 5.5977 Evaluate side-chains 87 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 120 SER Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 198 VAL Chi-restraints excluded: chain P residue 217 LEU Chi-restraints excluded: chain P residue 252 MET Chi-restraints excluded: chain P residue 260 ILE Chi-restraints excluded: chain P residue 344 VAL Chi-restraints excluded: chain P residue 347 VAL Chi-restraints excluded: chain P residue 348 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.4909 > 50: distance: 11 - 193: 22.474 distance: 36 - 197: 25.951 distance: 39 - 194: 26.313 distance: 53 - 179: 31.152 distance: 56 - 176: 18.996 distance: 71 - 159: 11.529 distance: 74 - 156: 20.834 distance: 114 - 136: 8.035 distance: 128 - 131: 3.279 distance: 129 - 130: 5.990 distance: 129 - 136: 4.073 distance: 136 - 137: 3.778 distance: 137 - 138: 7.285 distance: 138 - 139: 22.893 distance: 138 - 144: 21.827 distance: 140 - 141: 4.593 distance: 144 - 145: 13.168 distance: 145 - 146: 7.867 distance: 145 - 148: 15.178 distance: 146 - 147: 3.515 distance: 146 - 151: 24.838 distance: 148 - 149: 14.495 distance: 148 - 150: 13.927 distance: 151 - 152: 18.126 distance: 152 - 153: 37.327 distance: 152 - 155: 9.181 distance: 153 - 154: 30.465 distance: 153 - 156: 29.823 distance: 156 - 157: 41.064 distance: 157 - 158: 17.793 distance: 157 - 160: 14.008 distance: 158 - 159: 12.719 distance: 158 - 164: 23.414 distance: 160 - 161: 17.596 distance: 161 - 162: 7.250 distance: 161 - 163: 15.016 distance: 164 - 165: 48.051 distance: 165 - 166: 40.548 distance: 165 - 168: 40.422 distance: 166 - 167: 28.492 distance: 166 - 176: 17.977 distance: 168 - 169: 17.484 distance: 169 - 170: 30.900 distance: 169 - 171: 29.317 distance: 170 - 172: 16.113 distance: 171 - 173: 13.322 distance: 172 - 174: 39.062 distance: 173 - 174: 16.593 distance: 174 - 175: 18.556 distance: 176 - 177: 4.885 distance: 177 - 178: 19.886 distance: 177 - 180: 13.617 distance: 178 - 179: 19.888 distance: 178 - 188: 13.276 distance: 180 - 181: 26.871 distance: 181 - 182: 15.878 distance: 181 - 183: 19.584 distance: 182 - 184: 11.070 distance: 183 - 185: 13.647 distance: 184 - 186: 16.490 distance: 185 - 186: 12.428 distance: 186 - 187: 13.625 distance: 188 - 189: 11.685 distance: 189 - 190: 19.853 distance: 189 - 192: 10.490 distance: 190 - 191: 41.930 distance: 190 - 194: 15.628 distance: 192 - 193: 24.042 distance: 194 - 195: 43.140 distance: 195 - 196: 28.570 distance: 195 - 198: 28.363 distance: 196 - 197: 27.803 distance: 196 - 199: 21.960 distance: 199 - 200: 25.109 distance: 200 - 201: 10.262 distance: 200 - 203: 11.076 distance: 201 - 202: 24.924 distance: 201 - 210: 31.498 distance: 203 - 204: 13.564 distance: 204 - 205: 14.234 distance: 205 - 206: 13.555 distance: 206 - 207: 26.248 distance: 207 - 208: 21.134 distance: 207 - 209: 21.116