Starting phenix.real_space_refine on Tue Jan 13 10:07:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g4h_29720/01_2026/8g4h_29720.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g4h_29720/01_2026/8g4h_29720.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8g4h_29720/01_2026/8g4h_29720.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g4h_29720/01_2026/8g4h_29720.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g4h_29720/01_2026/8g4h_29720.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g4h_29720/01_2026/8g4h_29720.map" } resolution = 2.87 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= -0.001 sd= 0.062 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 6 5.16 5 C 1581 2.51 5 N 442 2.21 5 O 501 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2533 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1159 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 3, 'TRANS': 148} Chain: "B" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1345 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 4, 'TRANS': 163} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.68, per 1000 atoms: 0.27 Number of scatterers: 2533 At special positions: 0 Unit cell: (74.8, 53.9, 69.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 6 16.00 P 2 15.00 Mg 1 11.99 O 501 8.00 N 442 7.00 C 1581 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.14 Conformation dependent library (CDL) restraints added in 59.2 milliseconds 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 594 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 1 sheets defined 55.6% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 169 through 178 Processing helix chain 'A' and resid 179 through 190 removed outlier: 3.502A pdb=" N VAL A 183 " --> pdb=" O GLN A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 211 Processing helix chain 'A' and resid 212 through 223 Processing helix chain 'A' and resid 235 through 244 Processing helix chain 'A' and resid 245 through 255 removed outlier: 3.521A pdb=" N TRP A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 277 Processing helix chain 'A' and resid 278 through 288 Processing helix chain 'A' and resid 301 through 310 Processing helix chain 'A' and resid 311 through 320 Processing helix chain 'B' and resid 15 through 26 Processing helix chain 'B' and resid 65 through 75 Processing helix chain 'B' and resid 87 through 104 removed outlier: 3.558A pdb=" N ILE B 93 " --> pdb=" O SER B 89 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N HIS B 94 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N HIS B 95 " --> pdb=" O GLU B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 138 removed outlier: 3.583A pdb=" N ALA B 130 " --> pdb=" O ASP B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 168 removed outlier: 3.934A pdb=" N PHE B 156 " --> pdb=" O VAL B 152 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 38 through 46 removed outlier: 3.731A pdb=" N ASP B 38 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N GLY B 77 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LYS B 5 " --> pdb=" O GLY B 77 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N LEU B 79 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL B 7 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N VAL B 81 " --> pdb=" O VAL B 7 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL B 9 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N ALA B 83 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N PHE B 78 " --> pdb=" O VAL B 112 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N VAL B 114 " --> pdb=" O PHE B 78 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU B 80 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ASN B 116 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N PHE B 82 " --> pdb=" O ASN B 116 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N ILE B 142 " --> pdb=" O MET B 111 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU B 113 " --> pdb=" O ILE B 142 " (cutoff:3.500A) 125 hydrogen bonds defined for protein. 372 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: 0.38 Time building geometry restraints manager: 0.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 868 1.34 - 1.46: 479 1.46 - 1.58: 1211 1.58 - 1.69: 3 1.69 - 1.81: 11 Bond restraints: 2572 Sorted by residual: bond pdb=" C5 GDP B 201 " pdb=" C4 GDP B 201 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.24e+00 bond pdb=" CA VAL B 109 " pdb=" CB VAL B 109 " ideal model delta sigma weight residual 1.537 1.528 0.009 1.29e-02 6.01e+03 4.74e-01 bond pdb=" N VAL B 109 " pdb=" CA VAL B 109 " ideal model delta sigma weight residual 1.461 1.469 -0.008 1.23e-02 6.61e+03 3.72e-01 bond pdb=" C3' GDP B 201 " pdb=" C2' GDP B 201 " ideal model delta sigma weight residual 1.524 1.512 0.012 2.00e-02 2.50e+03 3.49e-01 bond pdb=" N GLU B 107 " pdb=" CA GLU B 107 " ideal model delta sigma weight residual 1.463 1.469 -0.006 1.08e-02 8.57e+03 3.20e-01 ... (remaining 2567 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 3381 1.11 - 2.21: 74 2.21 - 3.32: 21 3.32 - 4.43: 3 4.43 - 5.53: 2 Bond angle restraints: 3481 Sorted by residual: angle pdb=" N ASP B 105 " pdb=" CA ASP B 105 " pdb=" CB ASP B 105 " ideal model delta sigma weight residual 113.65 110.52 3.13 1.47e+00 4.63e-01 4.53e+00 angle pdb=" C3' GDP B 201 " pdb=" C2' GDP B 201 " pdb=" C1' GDP B 201 " ideal model delta sigma weight residual 111.00 105.47 5.53 3.00e+00 1.11e-01 3.40e+00 angle pdb=" CA GLY A 277 " pdb=" C GLY A 277 " pdb=" N HIS A 278 " ideal model delta sigma weight residual 118.50 116.72 1.78 9.90e-01 1.02e+00 3.23e+00 angle pdb=" CA SER B 106 " pdb=" C SER B 106 " pdb=" N GLU B 107 " ideal model delta sigma weight residual 115.67 117.87 -2.20 1.23e+00 6.61e-01 3.19e+00 angle pdb=" C4' GDP B 201 " pdb=" C3' GDP B 201 " pdb=" C2' GDP B 201 " ideal model delta sigma weight residual 111.00 105.66 5.34 3.00e+00 1.11e-01 3.17e+00 ... (remaining 3476 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.77: 1381 12.77 - 25.54: 115 25.54 - 38.31: 39 38.31 - 51.08: 11 51.08 - 63.85: 3 Dihedral angle restraints: 1549 sinusoidal: 627 harmonic: 922 Sorted by residual: dihedral pdb=" CA ASP B 105 " pdb=" C ASP B 105 " pdb=" N SER B 106 " pdb=" CA SER B 106 " ideal model delta harmonic sigma weight residual 180.00 163.86 16.14 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" N LEU B 113 " pdb=" CA LEU B 113 " pdb=" CB LEU B 113 " pdb=" CG LEU B 113 " ideal model delta sinusoidal sigma weight residual -180.00 -123.98 -56.02 3 1.50e+01 4.44e-03 9.38e+00 dihedral pdb=" N ARG A 222 " pdb=" CA ARG A 222 " pdb=" CB ARG A 222 " pdb=" CG ARG A 222 " ideal model delta sinusoidal sigma weight residual -60.00 -115.55 55.55 3 1.50e+01 4.44e-03 9.35e+00 ... (remaining 1546 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 228 0.024 - 0.048: 99 0.048 - 0.072: 39 0.072 - 0.097: 16 0.097 - 0.121: 13 Chirality restraints: 395 Sorted by residual: chirality pdb=" CA ILE B 55 " pdb=" N ILE B 55 " pdb=" C ILE B 55 " pdb=" CB ILE B 55 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.65e-01 chirality pdb=" CA ILE B 46 " pdb=" N ILE B 46 " pdb=" C ILE B 46 " pdb=" CB ILE B 46 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.42e-01 chirality pdb=" CA VAL B 8 " pdb=" N VAL B 8 " pdb=" C VAL B 8 " pdb=" CB VAL B 8 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.25e-01 ... (remaining 392 not shown) Planarity restraints: 452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 268 " -0.026 5.00e-02 4.00e+02 3.91e-02 2.45e+00 pdb=" N PRO A 269 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 269 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 269 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 109 " 0.024 5.00e-02 4.00e+02 3.67e-02 2.16e+00 pdb=" N PRO B 110 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 110 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 110 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 235 " -0.024 5.00e-02 4.00e+02 3.59e-02 2.07e+00 pdb=" N PRO A 236 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 236 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 236 " -0.020 5.00e-02 4.00e+02 ... (remaining 449 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 25 2.60 - 3.17: 2055 3.17 - 3.75: 3743 3.75 - 4.32: 5397 4.32 - 4.90: 8989 Nonbonded interactions: 20209 Sorted by model distance: nonbonded pdb=" OG SER B 17 " pdb="MG MG B 202 " model vdw 2.022 2.170 nonbonded pdb=" O3B GDP B 201 " pdb="MG MG B 202 " model vdw 2.257 2.170 nonbonded pdb=" OH TYR A 232 " pdb=" OE2 GLU A 265 " model vdw 2.297 3.040 nonbonded pdb=" OE1 GLN B 61 " pdb=" NH1 ARG B 68 " model vdw 2.316 3.120 nonbonded pdb=" OG1 THR A 202 " pdb=" ND1 HIS A 205 " model vdw 2.353 3.120 ... (remaining 20204 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: 1.430 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: 0.020 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 3.840 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:6.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 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 : 0.002 0.022 2572 Z= 0.106 Angle : 0.467 5.532 3481 Z= 0.249 Chirality : 0.037 0.121 395 Planarity : 0.004 0.039 452 Dihedral : 11.451 63.854 955 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.51 % Allowed : 6.79 % Favored : 91.70 % 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 are not related in a simple way. whole: 1.07 (0.45), residues: 316 helix: 1.67 (0.39), residues: 170 sheet: 1.02 (0.66), residues: 47 loop : -1.17 (0.56), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 176 TYR 0.006 0.001 TYR B 32 PHE 0.006 0.001 PHE B 82 TRP 0.003 0.001 TRP A 255 HIS 0.003 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 2572) covalent geometry : angle 0.46710 ( 3481) hydrogen bonds : bond 0.15239 ( 125) hydrogen bonds : angle 5.76028 ( 372) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.061 Fit side-chains REVERT: A 173 GLU cc_start: 0.8077 (mp0) cc_final: 0.7804 (mm-30) REVERT: B 68 ARG cc_start: 0.7972 (ttp80) cc_final: 0.7702 (ttp-170) REVERT: B 108 ASP cc_start: 0.5788 (t0) cc_final: 0.5508 (t0) outliers start: 4 outliers final: 3 residues processed: 54 average time/residue: 0.5217 time to fit residues: 28.8045 Evaluate side-chains 39 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 113 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 27 optimal weight: 3.9990 chunk 12 optimal weight: 0.0770 chunk 24 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 0.1980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN ** B 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.173641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.146890 restraints weight = 3017.311| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.87 r_work: 0.3556 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2572 Z= 0.109 Angle : 0.490 5.936 3481 Z= 0.248 Chirality : 0.038 0.122 395 Planarity : 0.004 0.048 452 Dihedral : 6.834 54.749 361 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.89 % Allowed : 15.47 % Favored : 82.64 % 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 are not related in a simple way. whole: 1.27 (0.45), residues: 316 helix: 2.04 (0.39), residues: 170 sheet: 0.78 (0.64), residues: 47 loop : -1.31 (0.55), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 68 TYR 0.007 0.001 TYR B 157 PHE 0.005 0.001 PHE B 82 TRP 0.003 0.001 TRP A 255 HIS 0.004 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 2572) covalent geometry : angle 0.49004 ( 3481) hydrogen bonds : bond 0.03200 ( 125) hydrogen bonds : angle 4.58758 ( 372) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.060 Fit side-chains REVERT: B 24 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.7659 (mp) REVERT: B 108 ASP cc_start: 0.5652 (t0) cc_final: 0.5086 (t0) outliers start: 5 outliers final: 3 residues processed: 43 average time/residue: 0.5270 time to fit residues: 23.2081 Evaluate side-chains 40 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 113 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 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 260 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.170778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.144052 restraints weight = 3051.605| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.86 r_work: 0.3528 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2572 Z= 0.135 Angle : 0.517 5.905 3481 Z= 0.263 Chirality : 0.039 0.126 395 Planarity : 0.005 0.041 452 Dihedral : 7.143 53.061 361 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.89 % Allowed : 16.23 % Favored : 81.89 % 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 are not related in a simple way. whole: 1.10 (0.44), residues: 316 helix: 1.97 (0.39), residues: 170 sheet: 0.50 (0.62), residues: 47 loop : -1.40 (0.53), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 123 TYR 0.008 0.001 TYR B 32 PHE 0.006 0.001 PHE B 82 TRP 0.006 0.001 TRP A 255 HIS 0.004 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 2572) covalent geometry : angle 0.51665 ( 3481) hydrogen bonds : bond 0.03460 ( 125) hydrogen bonds : angle 4.58399 ( 372) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.118 Fit side-chains REVERT: B 24 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.7828 (mp) REVERT: B 108 ASP cc_start: 0.5676 (t0) cc_final: 0.5280 (t0) outliers start: 5 outliers final: 3 residues processed: 42 average time/residue: 0.4808 time to fit residues: 20.7472 Evaluate side-chains 40 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 126 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 2 optimal weight: 0.0370 chunk 6 optimal weight: 0.0770 chunk 10 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 22 optimal weight: 0.3980 chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 overall best weight: 0.3216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.174142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.147417 restraints weight = 3014.344| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 1.88 r_work: 0.3567 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2572 Z= 0.091 Angle : 0.460 5.690 3481 Z= 0.232 Chirality : 0.037 0.117 395 Planarity : 0.004 0.037 452 Dihedral : 6.198 55.056 359 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.89 % Allowed : 16.98 % Favored : 81.13 % 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 are not related in a simple way. whole: 1.48 (0.45), residues: 316 helix: 2.33 (0.39), residues: 170 sheet: 0.66 (0.61), residues: 47 loop : -1.36 (0.53), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 68 TYR 0.005 0.001 TYR A 210 PHE 0.005 0.001 PHE B 82 TRP 0.001 0.000 TRP A 255 HIS 0.003 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00198 ( 2572) covalent geometry : angle 0.45952 ( 3481) hydrogen bonds : bond 0.02542 ( 125) hydrogen bonds : angle 4.24145 ( 372) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.098 Fit side-chains REVERT: A 229 ASP cc_start: 0.7961 (m-30) cc_final: 0.7642 (m-30) REVERT: B 108 ASP cc_start: 0.5713 (t0) cc_final: 0.5426 (t0) outliers start: 5 outliers final: 2 residues processed: 42 average time/residue: 0.5800 time to fit residues: 24.9589 Evaluate side-chains 38 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain B residue 35 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 7 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 26 optimal weight: 0.1980 chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 19 optimal weight: 0.0040 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.172061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.145396 restraints weight = 3036.115| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 1.86 r_work: 0.3539 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2572 Z= 0.116 Angle : 0.500 5.841 3481 Z= 0.253 Chirality : 0.039 0.120 395 Planarity : 0.004 0.039 452 Dihedral : 6.438 53.225 359 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.40 % Allowed : 16.60 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.44), residues: 316 helix: 2.19 (0.39), residues: 170 sheet: 0.67 (0.61), residues: 47 loop : -1.50 (0.51), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 164 TYR 0.006 0.001 TYR B 157 PHE 0.004 0.001 PHE B 82 TRP 0.003 0.001 TRP A 255 HIS 0.004 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 2572) covalent geometry : angle 0.49980 ( 3481) hydrogen bonds : bond 0.03040 ( 125) hydrogen bonds : angle 4.35368 ( 372) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.103 Fit side-chains REVERT: B 24 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.7737 (mp) REVERT: B 108 ASP cc_start: 0.5670 (t0) cc_final: 0.5235 (t0) outliers start: 9 outliers final: 6 residues processed: 44 average time/residue: 0.4927 time to fit residues: 22.2974 Evaluate side-chains 43 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 136 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 18 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 20 optimal weight: 0.0870 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.3953 r_free = 0.3953 target = 0.172221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.145507 restraints weight = 3039.102| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 1.87 r_work: 0.3539 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2572 Z= 0.114 Angle : 0.502 5.814 3481 Z= 0.253 Chirality : 0.039 0.119 395 Planarity : 0.004 0.039 452 Dihedral : 6.449 54.088 359 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.02 % Allowed : 16.98 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.44), residues: 316 helix: 2.18 (0.39), residues: 170 sheet: 0.71 (0.61), residues: 47 loop : -1.47 (0.52), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 68 TYR 0.009 0.001 TYR B 157 PHE 0.005 0.001 PHE B 82 TRP 0.002 0.001 TRP A 255 HIS 0.004 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 2572) covalent geometry : angle 0.50179 ( 3481) hydrogen bonds : bond 0.02971 ( 125) hydrogen bonds : angle 4.35673 ( 372) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.117 Fit side-chains REVERT: A 229 ASP cc_start: 0.7931 (m-30) cc_final: 0.7597 (m-30) REVERT: B 24 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.7706 (mp) REVERT: B 108 ASP cc_start: 0.5679 (t0) cc_final: 0.5203 (t0) outliers start: 8 outliers final: 3 residues processed: 40 average time/residue: 0.5232 time to fit residues: 21.5347 Evaluate side-chains 40 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 35 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 30 optimal weight: 0.0000 chunk 15 optimal weight: 0.6980 chunk 11 optimal weight: 0.2980 chunk 23 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 16 optimal weight: 0.0000 overall best weight: 0.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.174885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.148158 restraints weight = 3009.080| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 1.87 r_work: 0.3567 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2572 Z= 0.091 Angle : 0.468 5.709 3481 Z= 0.236 Chirality : 0.037 0.116 395 Planarity : 0.004 0.039 452 Dihedral : 6.112 54.646 359 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.02 % Allowed : 17.74 % Favored : 79.25 % 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 are not related in a simple way. whole: 1.55 (0.45), residues: 316 helix: 2.40 (0.39), residues: 170 sheet: 0.78 (0.60), residues: 47 loop : -1.39 (0.52), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 68 TYR 0.006 0.001 TYR A 210 PHE 0.006 0.001 PHE B 82 TRP 0.001 0.000 TRP A 255 HIS 0.004 0.001 HIS B 27 Details of bonding type rmsd covalent geometry : bond 0.00203 ( 2572) covalent geometry : angle 0.46781 ( 3481) hydrogen bonds : bond 0.02493 ( 125) hydrogen bonds : angle 4.15291 ( 372) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.122 Fit side-chains REVERT: A 254 ARG cc_start: 0.7162 (mtp180) cc_final: 0.6791 (ttm110) REVERT: A 300 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7200 (tptm) REVERT: B 108 ASP cc_start: 0.5372 (t0) cc_final: 0.4978 (t0) outliers start: 8 outliers final: 3 residues processed: 41 average time/residue: 0.5629 time to fit residues: 23.6232 Evaluate side-chains 38 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 71 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 25 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 19 optimal weight: 0.0980 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.172075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.145575 restraints weight = 3060.031| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.84 r_work: 0.3545 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2572 Z= 0.121 Angle : 0.508 5.853 3481 Z= 0.257 Chirality : 0.039 0.127 395 Planarity : 0.004 0.039 452 Dihedral : 6.467 53.630 359 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.89 % Allowed : 19.62 % Favored : 78.49 % 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 are not related in a simple way. whole: 1.37 (0.45), residues: 316 helix: 2.25 (0.39), residues: 170 sheet: 0.69 (0.60), residues: 47 loop : -1.44 (0.53), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 68 TYR 0.006 0.001 TYR B 32 PHE 0.005 0.001 PHE B 82 TRP 0.004 0.001 TRP A 255 HIS 0.004 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 2572) covalent geometry : angle 0.50845 ( 3481) hydrogen bonds : bond 0.03002 ( 125) hydrogen bonds : angle 4.28532 ( 372) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.099 Fit side-chains REVERT: A 300 LYS cc_start: 0.7632 (OUTLIER) cc_final: 0.7211 (tptm) REVERT: B 108 ASP cc_start: 0.5632 (t0) cc_final: 0.5377 (t0) outliers start: 5 outliers final: 4 residues processed: 38 average time/residue: 0.5386 time to fit residues: 20.9965 Evaluate side-chains 40 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 136 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 5 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 25 optimal weight: 0.3980 chunk 26 optimal weight: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 = 0.3970 r_free = 0.3970 target = 0.173783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.147297 restraints weight = 3063.475| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 1.87 r_work: 0.3547 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2572 Z= 0.107 Angle : 0.492 5.792 3481 Z= 0.249 Chirality : 0.038 0.122 395 Planarity : 0.004 0.039 452 Dihedral : 6.363 54.897 359 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.89 % Allowed : 20.75 % Favored : 77.36 % 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 are not related in a simple way. whole: 1.48 (0.45), residues: 316 helix: 2.35 (0.39), residues: 170 sheet: 0.86 (0.58), residues: 46 loop : -1.47 (0.53), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 68 TYR 0.006 0.001 TYR A 210 PHE 0.005 0.001 PHE B 82 TRP 0.001 0.001 TRP A 255 HIS 0.003 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 2572) covalent geometry : angle 0.49234 ( 3481) hydrogen bonds : bond 0.02774 ( 125) hydrogen bonds : angle 4.19955 ( 372) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.066 Fit side-chains REVERT: A 300 LYS cc_start: 0.7606 (OUTLIER) cc_final: 0.7194 (tptm) REVERT: B 108 ASP cc_start: 0.5371 (t0) cc_final: 0.5155 (t0) outliers start: 5 outliers final: 4 residues processed: 39 average time/residue: 0.5520 time to fit residues: 22.0379 Evaluate side-chains 41 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 136 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 15 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 8 optimal weight: 0.0170 chunk 10 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 27 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.172728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.145832 restraints weight = 3099.877| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.90 r_work: 0.3537 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2572 Z= 0.113 Angle : 0.503 5.810 3481 Z= 0.255 Chirality : 0.039 0.123 395 Planarity : 0.004 0.039 452 Dihedral : 6.453 54.776 359 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.26 % Allowed : 20.75 % Favored : 76.98 % 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 are not related in a simple way. whole: 1.40 (0.45), residues: 316 helix: 2.26 (0.39), residues: 171 sheet: 0.86 (0.58), residues: 46 loop : -1.52 (0.54), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 68 TYR 0.006 0.001 TYR A 210 PHE 0.005 0.001 PHE B 82 TRP 0.003 0.001 TRP A 255 HIS 0.004 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 2572) covalent geometry : angle 0.50278 ( 3481) hydrogen bonds : bond 0.02887 ( 125) hydrogen bonds : angle 4.22920 ( 372) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.111 Fit side-chains REVERT: A 300 LYS cc_start: 0.7615 (OUTLIER) cc_final: 0.7201 (tptm) REVERT: B 108 ASP cc_start: 0.5396 (t0) cc_final: 0.5023 (t0) outliers start: 6 outliers final: 5 residues processed: 40 average time/residue: 0.5640 time to fit residues: 23.0888 Evaluate side-chains 42 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 136 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 28 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN ** B 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.171068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.144511 restraints weight = 3060.328| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 1.86 r_work: 0.3540 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2572 Z= 0.133 Angle : 0.525 5.834 3481 Z= 0.267 Chirality : 0.040 0.126 395 Planarity : 0.004 0.039 452 Dihedral : 6.684 54.378 359 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.02 % Allowed : 20.00 % Favored : 76.98 % 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 are not related in a simple way. whole: 1.25 (0.45), residues: 316 helix: 2.13 (0.39), residues: 171 sheet: 0.77 (0.59), residues: 46 loop : -1.55 (0.54), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 68 TYR 0.006 0.001 TYR B 32 PHE 0.004 0.001 PHE B 82 TRP 0.004 0.001 TRP A 255 HIS 0.004 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 2572) covalent geometry : angle 0.52473 ( 3481) hydrogen bonds : bond 0.03181 ( 125) hydrogen bonds : angle 4.33664 ( 372) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1198.94 seconds wall clock time: 21 minutes 19.06 seconds (1279.06 seconds total)