Starting phenix.real_space_refine on Fri Aug 22 16:55:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c4b_45180/08_2025/9c4b_45180.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c4b_45180/08_2025/9c4b_45180.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9c4b_45180/08_2025/9c4b_45180.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c4b_45180/08_2025/9c4b_45180.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9c4b_45180/08_2025/9c4b_45180.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c4b_45180/08_2025/9c4b_45180.map" } resolution = 3.4 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= -0.000 sd= 0.042 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: 5 Type Number sf(0) Gaussians S 24 5.16 5 C 1950 2.51 5 N 525 2.21 5 O 581 1.98 5 H 3030 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 6110 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 6110 Classifications: {'peptide': 393} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 370} Chain breaks: 2 Time building chain proxies: 0.97, per 1000 atoms: 0.16 Number of scatterers: 6110 At special positions: 0 Unit cell: (81.9, 69.3, 78.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 O 581 8.00 N 525 7.00 C 1950 6.00 H 3030 1.00 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: 0.41 Conformation dependent library (CDL) restraints added in 156.4 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 730 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 3 sheets defined 44.5% alpha, 11.5% 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 70 through 77 removed outlier: 3.902A pdb=" N ALA A 74 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL A 77 " --> pdb=" O ASN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 109 Processing helix chain 'A' and resid 129 through 143 Processing helix chain 'A' and resid 154 through 163 Processing helix chain 'A' and resid 189 through 192 removed outlier: 3.578A pdb=" N ILE A 192 " --> pdb=" O GLN A 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 189 through 192' Processing helix chain 'A' and resid 198 through 210 Processing helix chain 'A' and resid 247 through 267 removed outlier: 3.683A pdb=" N SER A 265 " --> pdb=" O ASP A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 304 Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 324 through 336 removed outlier: 3.536A pdb=" N CYS A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 345 Processing helix chain 'A' and resid 352 through 356 removed outlier: 3.642A pdb=" N LEU A 356 " --> pdb=" O GLY A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 372 Processing helix chain 'A' and resid 385 through 391 Processing helix chain 'A' and resid 391 through 403 removed outlier: 3.627A pdb=" N LEU A 403 " --> pdb=" O ILE A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 422 through 428 removed outlier: 4.025A pdb=" N ARG A 426 " --> pdb=" O GLN A 422 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 38 removed outlier: 4.428A pdb=" N ILE A 18 " --> pdb=" O SER A 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 187 removed outlier: 3.574A pdb=" N VAL A 193 " --> pdb=" O ALA A 179 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 186 through 187 removed outlier: 5.817A pdb=" N LEU A 168 " --> pdb=" O ILE A 349 " (cutoff:3.500A) 129 hydrogen bonds defined for protein. 357 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.39 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3021 1.03 - 1.23: 13 1.23 - 1.42: 1310 1.42 - 1.62: 1797 1.62 - 1.81: 39 Bond restraints: 6180 Sorted by residual: bond pdb=" N VAL A 278 " pdb=" CA VAL A 278 " ideal model delta sigma weight residual 1.459 1.504 -0.045 1.25e-02 6.40e+03 1.29e+01 bond pdb=" N GLN A 281 " pdb=" CA GLN A 281 " ideal model delta sigma weight residual 1.458 1.490 -0.032 9.00e-03 1.23e+04 1.23e+01 bond pdb=" N VAL A 93 " pdb=" CA VAL A 93 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.10e-02 8.26e+03 1.03e+01 bond pdb=" N PHE A 210 " pdb=" CA PHE A 210 " ideal model delta sigma weight residual 1.455 1.494 -0.038 1.33e-02 5.65e+03 8.32e+00 bond pdb=" N GLU A 208 " pdb=" H GLU A 208 " ideal model delta sigma weight residual 0.860 0.914 -0.054 2.00e-02 2.50e+03 7.19e+00 ... (remaining 6175 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 11102 2.85 - 5.70: 52 5.70 - 8.56: 3 8.56 - 11.41: 1 11.41 - 14.26: 1 Bond angle restraints: 11159 Sorted by residual: angle pdb=" N GLN A 211 " pdb=" CA GLN A 211 " pdb=" C GLN A 211 " ideal model delta sigma weight residual 112.89 98.63 14.26 1.24e+00 6.50e-01 1.32e+02 angle pdb=" N ALA A 279 " pdb=" CA ALA A 279 " pdb=" C ALA A 279 " ideal model delta sigma weight residual 112.90 105.10 7.80 1.31e+00 5.83e-01 3.54e+01 angle pdb=" N PHE A 210 " pdb=" CA PHE A 210 " pdb=" C PHE A 210 " ideal model delta sigma weight residual 113.30 105.83 7.47 1.34e+00 5.57e-01 3.11e+01 angle pdb=" C PHE A 210 " pdb=" CA PHE A 210 " pdb=" CB PHE A 210 " ideal model delta sigma weight residual 110.17 119.40 -9.23 1.69e+00 3.50e-01 2.98e+01 angle pdb=" CA PHE A 210 " pdb=" CB PHE A 210 " pdb=" CG PHE A 210 " ideal model delta sigma weight residual 113.80 108.84 4.96 1.00e+00 1.00e+00 2.46e+01 ... (remaining 11154 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 2546 17.69 - 35.39: 255 35.39 - 53.08: 89 53.08 - 70.77: 33 70.77 - 88.47: 9 Dihedral angle restraints: 2932 sinusoidal: 1599 harmonic: 1333 Sorted by residual: dihedral pdb=" C PHE A 210 " pdb=" N PHE A 210 " pdb=" CA PHE A 210 " pdb=" CB PHE A 210 " ideal model delta harmonic sigma weight residual -122.60 -131.87 9.27 0 2.50e+00 1.60e-01 1.37e+01 dihedral pdb=" CA LYS A 240 " pdb=" C LYS A 240 " pdb=" N GLU A 241 " pdb=" CA GLU A 241 " ideal model delta harmonic sigma weight residual 180.00 -162.58 -17.42 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ILE A 223 " pdb=" C ILE A 223 " pdb=" N ALA A 224 " pdb=" CA ALA A 224 " ideal model delta harmonic sigma weight residual 180.00 163.25 16.75 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 2929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 340 0.042 - 0.083: 86 0.083 - 0.125: 40 0.125 - 0.167: 4 0.167 - 0.209: 2 Chirality restraints: 472 Sorted by residual: chirality pdb=" CA PHE A 210 " pdb=" N PHE A 210 " pdb=" C PHE A 210 " pdb=" CB PHE A 210 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA MET A 92 " pdb=" N MET A 92 " pdb=" C MET A 92 " pdb=" CB MET A 92 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.75e-01 chirality pdb=" CA MET A 254 " pdb=" N MET A 254 " pdb=" C MET A 254 " pdb=" CB MET A 254 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.87e-01 ... (remaining 469 not shown) Planarity restraints: 922 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 211 " -0.254 2.00e-02 2.50e+03 3.24e-01 1.57e+03 pdb=" CD GLN A 211 " 0.023 2.00e-02 2.50e+03 pdb=" OE1 GLN A 211 " 0.241 2.00e-02 2.50e+03 pdb=" NE2 GLN A 211 " 0.005 2.00e-02 2.50e+03 pdb="HE21 GLN A 211 " 0.495 2.00e-02 2.50e+03 pdb="HE22 GLN A 211 " -0.510 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 281 " 0.141 2.00e-02 2.50e+03 1.55e-01 3.59e+02 pdb=" CD GLN A 281 " -0.004 2.00e-02 2.50e+03 pdb=" OE1 GLN A 281 " -0.139 2.00e-02 2.50e+03 pdb=" NE2 GLN A 281 " -0.002 2.00e-02 2.50e+03 pdb="HE21 GLN A 281 " -0.226 2.00e-02 2.50e+03 pdb="HE22 GLN A 281 " 0.230 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 210 " 0.059 2.00e-02 2.50e+03 2.66e-02 2.12e+01 pdb=" CG PHE A 210 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE A 210 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE A 210 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 PHE A 210 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 PHE A 210 " -0.029 2.00e-02 2.50e+03 pdb=" CZ PHE A 210 " 0.010 2.00e-02 2.50e+03 pdb=" HD1 PHE A 210 " -0.019 2.00e-02 2.50e+03 pdb=" HD2 PHE A 210 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE A 210 " 0.005 2.00e-02 2.50e+03 pdb=" HE2 PHE A 210 " 0.025 2.00e-02 2.50e+03 pdb=" HZ PHE A 210 " 0.011 2.00e-02 2.50e+03 ... (remaining 919 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 452 2.19 - 2.80: 12514 2.80 - 3.40: 17313 3.40 - 4.00: 22277 4.00 - 4.60: 33932 Nonbonded interactions: 86488 Sorted by model distance: nonbonded pdb=" O ALA A 74 " pdb="HH22 ARG A 79 " model vdw 1.593 2.450 nonbonded pdb=" O LEU A 168 " pdb=" H ILE A 349 " model vdw 1.647 2.450 nonbonded pdb=" OE1 GLU A 46 " pdb=" H ARG A 47 " model vdw 1.652 2.450 nonbonded pdb=" H ALA A 125 " pdb=" OD1 ASN A 128 " model vdw 1.675 2.450 nonbonded pdb=" O GLY A 12 " pdb=" HD1 HIS A 118 " model vdw 1.706 2.450 ... (remaining 86483 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 4.450 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: 0.020 Extract box with map and model: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.600 Find NCS groups from input model: 0.010 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 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 0.070 3150 Z= 0.241 Angle : 0.729 14.259 4272 Z= 0.462 Chirality : 0.047 0.209 472 Planarity : 0.004 0.044 554 Dihedral : 16.505 88.465 1163 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.78 % Allowed : 5.94 % Favored : 93.28 % Rotamer: Outliers : 0.89 % Allowed : 20.71 % Favored : 78.40 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % 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 (0.44), residues: 387 helix: 0.72 (0.46), residues: 148 sheet: -0.65 (0.74), residues: 55 loop : -1.01 (0.46), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 389 TYR 0.006 0.001 TYR A 253 PHE 0.045 0.002 PHE A 210 TRP 0.008 0.001 TRP A 410 HIS 0.002 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 3150) covalent geometry : angle 0.72904 ( 4272) hydrogen bonds : bond 0.20046 ( 127) hydrogen bonds : angle 7.87130 ( 357) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 TYR cc_start: 0.6051 (OUTLIER) cc_final: 0.5728 (t80) outliers start: 3 outliers final: 0 residues processed: 62 average time/residue: 0.1280 time to fit residues: 9.6230 Evaluate side-chains 56 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.151029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.131590 restraints weight = 18333.412| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.84 r_work: 0.3717 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3150 Z= 0.167 Angle : 0.588 5.371 4272 Z= 0.318 Chirality : 0.045 0.157 472 Planarity : 0.005 0.046 554 Dihedral : 5.329 29.380 426 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.78 % Allowed : 6.46 % Favored : 92.76 % Rotamer: Outliers : 2.07 % Allowed : 19.53 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.43 (0.44), residues: 387 helix: 0.72 (0.43), residues: 156 sheet: -0.46 (0.77), residues: 55 loop : -1.10 (0.47), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 24 TYR 0.018 0.001 TYR A 253 PHE 0.012 0.002 PHE A 210 TRP 0.007 0.001 TRP A 410 HIS 0.006 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 3150) covalent geometry : angle 0.58828 ( 4272) hydrogen bonds : bond 0.04835 ( 127) hydrogen bonds : angle 6.01043 ( 357) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASP cc_start: 0.7196 (OUTLIER) cc_final: 0.6897 (m-30) outliers start: 7 outliers final: 4 residues processed: 63 average time/residue: 0.1280 time to fit residues: 9.8048 Evaluate side-chains 61 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 362 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 37 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 6 optimal weight: 0.1980 chunk 35 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 chunk 9 optimal weight: 0.0980 chunk 2 optimal weight: 0.5980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.4053 r_free = 0.4053 target = 0.151439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.132629 restraints weight = 17937.397| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.80 r_work: 0.3730 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3150 Z= 0.117 Angle : 0.534 5.244 4272 Z= 0.283 Chirality : 0.043 0.147 472 Planarity : 0.004 0.042 554 Dihedral : 4.980 27.487 424 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.46 % Favored : 93.02 % Rotamer: Outliers : 2.37 % Allowed : 20.41 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.38 (0.44), residues: 387 helix: 0.84 (0.43), residues: 154 sheet: -0.44 (0.76), residues: 60 loop : -1.16 (0.47), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 24 TYR 0.009 0.001 TYR A 253 PHE 0.013 0.001 PHE A 262 TRP 0.011 0.001 TRP A 410 HIS 0.002 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 3150) covalent geometry : angle 0.53450 ( 4272) hydrogen bonds : bond 0.04065 ( 127) hydrogen bonds : angle 5.58045 ( 357) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 LYS cc_start: 0.8373 (mttm) cc_final: 0.7967 (mmtp) REVERT: A 254 MET cc_start: 0.8620 (mmp) cc_final: 0.8328 (mmp) REVERT: A 282 MET cc_start: 0.3950 (mmp) cc_final: 0.3737 (mmm) outliers start: 8 outliers final: 4 residues processed: 67 average time/residue: 0.1218 time to fit residues: 9.8621 Evaluate side-chains 62 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 392 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 8 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 38 optimal weight: 0.0010 chunk 1 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 2 optimal weight: 0.0270 overall best weight: 0.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.152734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.133196 restraints weight = 18369.833| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.88 r_work: 0.3726 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3150 Z= 0.111 Angle : 0.522 4.815 4272 Z= 0.274 Chirality : 0.043 0.140 472 Planarity : 0.004 0.042 554 Dihedral : 4.847 25.584 424 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.46 % Favored : 93.02 % Rotamer: Outliers : 2.07 % Allowed : 21.89 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.41 (0.45), residues: 387 helix: 0.84 (0.43), residues: 157 sheet: -0.59 (0.74), residues: 60 loop : -1.17 (0.49), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 79 TYR 0.005 0.001 TYR A 68 PHE 0.012 0.001 PHE A 262 TRP 0.013 0.002 TRP A 96 HIS 0.002 0.000 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 3150) covalent geometry : angle 0.52152 ( 4272) hydrogen bonds : bond 0.03557 ( 127) hydrogen bonds : angle 5.37626 ( 357) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.5840 (mmp-170) cc_final: 0.5544 (mmp-170) REVERT: A 90 ASN cc_start: 0.7940 (t0) cc_final: 0.7559 (t0) outliers start: 7 outliers final: 7 residues processed: 65 average time/residue: 0.1401 time to fit residues: 10.7792 Evaluate side-chains 66 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 110 HIS Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 392 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 15 optimal weight: 0.6980 chunk 6 optimal weight: 0.1980 chunk 26 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 29 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4064 r_free = 0.4064 target = 0.152518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.132681 restraints weight = 18537.802| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.88 r_work: 0.3719 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3150 Z= 0.118 Angle : 0.516 4.777 4272 Z= 0.271 Chirality : 0.042 0.137 472 Planarity : 0.004 0.042 554 Dihedral : 4.832 24.115 424 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.46 % Favored : 93.02 % Rotamer: Outliers : 2.96 % Allowed : 21.60 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.42 (0.45), residues: 387 helix: 0.90 (0.44), residues: 157 sheet: -0.67 (0.72), residues: 60 loop : -1.21 (0.49), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 79 TYR 0.006 0.001 TYR A 107 PHE 0.011 0.001 PHE A 262 TRP 0.011 0.002 TRP A 96 HIS 0.002 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 3150) covalent geometry : angle 0.51600 ( 4272) hydrogen bonds : bond 0.03322 ( 127) hydrogen bonds : angle 5.20532 ( 357) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.5820 (mmp-170) cc_final: 0.5514 (mmp-170) REVERT: A 90 ASN cc_start: 0.7905 (t0) cc_final: 0.7522 (t0) outliers start: 10 outliers final: 9 residues processed: 67 average time/residue: 0.1121 time to fit residues: 9.1998 Evaluate side-chains 67 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 398 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 31 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 15 optimal weight: 0.4980 chunk 7 optimal weight: 0.7980 chunk 33 optimal weight: 0.3980 chunk 8 optimal weight: 0.3980 chunk 30 optimal weight: 0.1980 chunk 12 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 = 0.4074 r_free = 0.4074 target = 0.153329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.133590 restraints weight = 18203.486| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.86 r_work: 0.3731 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3150 Z= 0.104 Angle : 0.503 4.505 4272 Z= 0.261 Chirality : 0.043 0.134 472 Planarity : 0.004 0.043 554 Dihedral : 4.627 22.475 424 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.46 % Favored : 93.02 % Rotamer: Outliers : 2.96 % Allowed : 21.89 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.31 (0.45), residues: 387 helix: 1.04 (0.44), residues: 157 sheet: -0.73 (0.72), residues: 60 loop : -1.17 (0.49), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 389 TYR 0.006 0.001 TYR A 68 PHE 0.011 0.001 PHE A 262 TRP 0.012 0.001 TRP A 96 HIS 0.002 0.000 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 3150) covalent geometry : angle 0.50251 ( 4272) hydrogen bonds : bond 0.03116 ( 127) hydrogen bonds : angle 5.01606 ( 357) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.5776 (mmp-170) cc_final: 0.5477 (mmp-170) REVERT: A 70 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7734 (mm) REVERT: A 90 ASN cc_start: 0.7858 (t0) cc_final: 0.7508 (t0) outliers start: 10 outliers final: 7 residues processed: 69 average time/residue: 0.1146 time to fit residues: 9.7388 Evaluate side-chains 68 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 110 HIS Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 398 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 11 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 19 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4056 r_free = 0.4056 target = 0.151884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.132193 restraints weight = 18281.254| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.82 r_work: 0.3709 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3150 Z= 0.142 Angle : 0.518 4.633 4272 Z= 0.272 Chirality : 0.042 0.137 472 Planarity : 0.004 0.043 554 Dihedral : 4.706 21.664 424 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.46 % Favored : 93.28 % Rotamer: Outliers : 2.96 % Allowed : 20.71 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.42 (0.45), residues: 387 helix: 1.02 (0.44), residues: 157 sheet: -0.81 (0.70), residues: 60 loop : -1.30 (0.49), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 79 TYR 0.016 0.001 TYR A 107 PHE 0.011 0.001 PHE A 262 TRP 0.009 0.001 TRP A 96 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 3150) covalent geometry : angle 0.51771 ( 4272) hydrogen bonds : bond 0.03230 ( 127) hydrogen bonds : angle 5.06610 ( 357) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.5805 (mmp-170) cc_final: 0.5507 (mmp-170) REVERT: A 70 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7796 (mm) REVERT: A 90 ASN cc_start: 0.7856 (t0) cc_final: 0.7512 (t0) outliers start: 10 outliers final: 7 residues processed: 65 average time/residue: 0.1199 time to fit residues: 9.4503 Evaluate side-chains 62 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 110 HIS Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 398 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 30 optimal weight: 0.9990 chunk 27 optimal weight: 0.0870 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 0 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 9 optimal weight: 0.4980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.151851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.132856 restraints weight = 17920.107| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.76 r_work: 0.3724 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3150 Z= 0.114 Angle : 0.503 4.479 4272 Z= 0.262 Chirality : 0.042 0.136 472 Planarity : 0.004 0.043 554 Dihedral : 4.636 20.978 424 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.46 % Favored : 93.28 % Rotamer: Outliers : 2.66 % Allowed : 21.01 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.31 (0.45), residues: 387 helix: 1.10 (0.44), residues: 154 sheet: -0.75 (0.71), residues: 60 loop : -1.18 (0.49), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 389 TYR 0.010 0.001 TYR A 107 PHE 0.015 0.001 PHE A 262 TRP 0.007 0.001 TRP A 410 HIS 0.002 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 3150) covalent geometry : angle 0.50319 ( 4272) hydrogen bonds : bond 0.03137 ( 127) hydrogen bonds : angle 4.96568 ( 357) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.5713 (mmp-170) cc_final: 0.5413 (mmp-170) REVERT: A 70 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7771 (mm) REVERT: A 90 ASN cc_start: 0.7867 (t0) cc_final: 0.7529 (t0) REVERT: A 248 ARG cc_start: 0.6746 (tpt170) cc_final: 0.6534 (tpm170) outliers start: 9 outliers final: 6 residues processed: 66 average time/residue: 0.1252 time to fit residues: 10.0900 Evaluate side-chains 66 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 110 HIS Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 398 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 10 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 21 optimal weight: 0.0870 chunk 2 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 = 0.4063 r_free = 0.4063 target = 0.152141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.132555 restraints weight = 18483.690| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.82 r_work: 0.3719 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3150 Z= 0.127 Angle : 0.514 4.564 4272 Z= 0.269 Chirality : 0.042 0.137 472 Planarity : 0.004 0.043 554 Dihedral : 4.643 20.337 424 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.72 % Favored : 93.02 % Rotamer: Outliers : 2.37 % Allowed : 20.41 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.45), residues: 387 helix: 1.27 (0.45), residues: 149 sheet: -0.83 (0.71), residues: 60 loop : -1.33 (0.47), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 389 TYR 0.008 0.001 TYR A 107 PHE 0.015 0.001 PHE A 262 TRP 0.006 0.001 TRP A 96 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 3150) covalent geometry : angle 0.51443 ( 4272) hydrogen bonds : bond 0.03127 ( 127) hydrogen bonds : angle 4.96109 ( 357) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.5747 (mmp-170) cc_final: 0.5454 (mmp-170) REVERT: A 70 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7777 (mm) REVERT: A 90 ASN cc_start: 0.7867 (t0) cc_final: 0.7581 (t0) outliers start: 8 outliers final: 6 residues processed: 66 average time/residue: 0.1236 time to fit residues: 9.8534 Evaluate side-chains 67 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 110 HIS Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 398 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 38 optimal weight: 0.0270 chunk 8 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 37 optimal weight: 0.0980 chunk 19 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 overall best weight: 0.4038 ------------------------------------------------------------------------------- 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 = 0.4074 r_free = 0.4074 target = 0.152966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.133421 restraints weight = 18385.277| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 2.85 r_work: 0.3735 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3150 Z= 0.104 Angle : 0.498 4.436 4272 Z= 0.258 Chirality : 0.042 0.136 472 Planarity : 0.004 0.042 554 Dihedral : 4.520 20.012 424 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.72 % Favored : 93.02 % Rotamer: Outliers : 1.78 % Allowed : 21.60 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.27 (0.44), residues: 387 helix: 1.31 (0.45), residues: 149 sheet: -0.72 (0.72), residues: 60 loop : -1.28 (0.47), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 389 TYR 0.006 0.001 TYR A 107 PHE 0.014 0.001 PHE A 262 TRP 0.011 0.001 TRP A 96 HIS 0.002 0.000 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 3150) covalent geometry : angle 0.49769 ( 4272) hydrogen bonds : bond 0.03015 ( 127) hydrogen bonds : angle 4.86072 ( 357) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7806 (mm) REVERT: A 90 ASN cc_start: 0.7874 (t0) cc_final: 0.7605 (t0) REVERT: A 248 ARG cc_start: 0.6713 (tpt170) cc_final: 0.6506 (tpm170) outliers start: 6 outliers final: 5 residues processed: 67 average time/residue: 0.1193 time to fit residues: 9.7446 Evaluate side-chains 64 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 110 HIS Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 398 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 11 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 27 optimal weight: 0.0970 chunk 23 optimal weight: 0.0970 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 15 optimal weight: 0.3980 chunk 35 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 30 optimal weight: 0.0980 overall best weight: 0.2776 ------------------------------------------------------------------------------- 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 = 0.4091 r_free = 0.4091 target = 0.154267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.134698 restraints weight = 18117.204| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.85 r_work: 0.3753 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3150 Z= 0.094 Angle : 0.487 4.467 4272 Z= 0.251 Chirality : 0.042 0.134 472 Planarity : 0.004 0.042 554 Dihedral : 4.305 19.261 424 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.20 % Favored : 93.54 % Rotamer: Outliers : 2.07 % Allowed : 21.30 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.10 (0.45), residues: 387 helix: 1.43 (0.45), residues: 149 sheet: -0.75 (0.72), residues: 60 loop : -1.11 (0.48), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 24 TYR 0.009 0.001 TYR A 68 PHE 0.013 0.001 PHE A 262 TRP 0.011 0.001 TRP A 410 HIS 0.001 0.000 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 3150) covalent geometry : angle 0.48693 ( 4272) hydrogen bonds : bond 0.02865 ( 127) hydrogen bonds : angle 4.77583 ( 357) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1743.56 seconds wall clock time: 30 minutes 13.19 seconds (1813.19 seconds total)