Starting phenix.real_space_refine on Wed Sep 17 02:58:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zf4_60050/09_2025/8zf4_60050.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zf4_60050/09_2025/8zf4_60050.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zf4_60050/09_2025/8zf4_60050.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zf4_60050/09_2025/8zf4_60050.map" model { file = "/net/cci-nas-00/data/ceres_data/8zf4_60050/09_2025/8zf4_60050.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zf4_60050/09_2025/8zf4_60050.cif" } resolution = 3.05 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= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 13 5.16 5 C 1352 2.51 5 N 356 2.21 5 O 352 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2073 Number of models: 1 Model: "" Number of chains: 1 Chain: "R" Number of atoms: 2073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2073 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'ARG:plan': 9, 'ASP:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 69 Time building chain proxies: 0.57, per 1000 atoms: 0.27 Number of scatterers: 2073 At special positions: 0 Unit cell: (60.45, 66.03, 73.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 13 16.00 O 352 8.00 N 356 7.00 C 1352 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 168 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.10 Conformation dependent library (CDL) restraints added in 51.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 528 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 0 sheets defined 77.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.03 Creating SS restraints... Processing helix chain 'R' and resid 18 through 47 removed outlier: 4.642A pdb=" N LEU R 32 " --> pdb=" O PHE R 28 " (cutoff:3.500A) Proline residue: R 33 - end of helix Processing helix chain 'R' and resid 51 through 79 removed outlier: 4.272A pdb=" N TYR R 55 " --> pdb=" O GLU R 51 " (cutoff:3.500A) Proline residue: R 71 - end of helix Processing helix chain 'R' and resid 86 through 121 removed outlier: 4.094A pdb=" N ARG R 91 " --> pdb=" O PRO R 87 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU R 92 " --> pdb=" O GLY R 88 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR R 102 " --> pdb=" O TYR R 98 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA R 105 " --> pdb=" O LEU R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 154 removed outlier: 3.770A pdb=" N SER R 133 " --> pdb=" O ARG R 129 " (cutoff:3.500A) Proline residue: R 151 - end of helix Processing helix chain 'R' and resid 177 through 191 Processing helix chain 'R' and resid 193 through 209 removed outlier: 3.602A pdb=" N LEU R 209 " --> pdb=" O LEU R 205 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 228 removed outlier: 3.652A pdb=" N ARG R 222 " --> pdb=" O ARG R 218 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL R 223 " --> pdb=" O GLU R 219 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 252 Proline residue: R 240 - end of helix Processing helix chain 'R' and resid 264 through 284 removed outlier: 4.428A pdb=" N GLU R 268 " --> pdb=" O GLY R 264 " (cutoff:3.500A) Proline residue: R 273 - end of helix removed outlier: 4.004A pdb=" N ALA R 280 " --> pdb=" O HIS R 276 " (cutoff:3.500A) Processing helix chain 'R' and resid 287 through 294 Processing helix chain 'R' and resid 299 through 303 154 hydrogen bonds defined for protein. 456 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: 0.17 Time building geometry restraints manager: 0.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 657 1.34 - 1.46: 555 1.46 - 1.59: 904 1.59 - 1.71: 0 1.71 - 1.84: 16 Bond restraints: 2132 Sorted by residual: bond pdb=" CB ASP R 81 " pdb=" CG ASP R 81 " ideal model delta sigma weight residual 1.516 1.432 0.084 2.50e-02 1.60e+03 1.13e+01 bond pdb=" C ARG R 129 " pdb=" N PRO R 130 " ideal model delta sigma weight residual 1.336 1.301 0.035 1.25e-02 6.40e+03 7.67e+00 bond pdb=" C ASP R 81 " pdb=" N VAL R 82 " ideal model delta sigma weight residual 1.331 1.294 0.036 1.40e-02 5.10e+03 6.69e+00 bond pdb=" CA ARG R 129 " pdb=" C ARG R 129 " ideal model delta sigma weight residual 1.524 1.501 0.022 1.26e-02 6.30e+03 3.15e+00 bond pdb=" C ARG R 129 " pdb=" O ARG R 129 " ideal model delta sigma weight residual 1.238 1.217 0.021 1.28e-02 6.10e+03 2.59e+00 ... (remaining 2127 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 2799 1.92 - 3.83: 89 3.83 - 5.75: 27 5.75 - 7.66: 6 7.66 - 9.58: 3 Bond angle restraints: 2924 Sorted by residual: angle pdb=" N PRO R 71 " pdb=" CA PRO R 71 " pdb=" C PRO R 71 " ideal model delta sigma weight residual 110.70 117.07 -6.37 1.22e+00 6.72e-01 2.72e+01 angle pdb=" N ASP R 81 " pdb=" CA ASP R 81 " pdb=" C ASP R 81 " ideal model delta sigma weight residual 111.30 117.61 -6.31 1.36e+00 5.41e-01 2.15e+01 angle pdb=" C ASP R 81 " pdb=" CA ASP R 81 " pdb=" CB ASP R 81 " ideal model delta sigma weight residual 111.95 105.25 6.70 1.50e+00 4.44e-01 2.00e+01 angle pdb=" N GLU R 156 " pdb=" CA GLU R 156 " pdb=" C GLU R 156 " ideal model delta sigma weight residual 110.80 102.42 8.38 2.13e+00 2.20e-01 1.55e+01 angle pdb=" CA PRO R 71 " pdb=" C PRO R 71 " pdb=" N PRO R 72 " ideal model delta sigma weight residual 117.93 122.49 -4.56 1.20e+00 6.94e-01 1.44e+01 ... (remaining 2919 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.52: 1052 12.52 - 25.04: 118 25.04 - 37.56: 44 37.56 - 50.08: 15 50.08 - 62.59: 2 Dihedral angle restraints: 1231 sinusoidal: 401 harmonic: 830 Sorted by residual: dihedral pdb=" CA LEU R 192 " pdb=" C LEU R 192 " pdb=" N LEU R 193 " pdb=" CA LEU R 193 " ideal model delta harmonic sigma weight residual 180.00 157.52 22.48 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA PRO R 71 " pdb=" C PRO R 71 " pdb=" N PRO R 72 " pdb=" CA PRO R 72 " ideal model delta harmonic sigma weight residual 180.00 160.18 19.82 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA PHE R 167 " pdb=" C PHE R 167 " pdb=" N CYS R 168 " pdb=" CA CYS R 168 " ideal model delta harmonic sigma weight residual 180.00 160.67 19.33 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 1228 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 236 0.049 - 0.097: 74 0.097 - 0.145: 20 0.145 - 0.194: 0 0.194 - 0.242: 1 Chirality restraints: 331 Sorted by residual: chirality pdb=" CA PRO R 71 " pdb=" N PRO R 71 " pdb=" C PRO R 71 " pdb=" CB PRO R 71 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA LEU R 19 " pdb=" N LEU R 19 " pdb=" C LEU R 19 " pdb=" CB LEU R 19 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CA TYR R 77 " pdb=" N TYR R 77 " pdb=" C TYR R 77 " pdb=" CB TYR R 77 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.54e-01 ... (remaining 328 not shown) Planarity restraints: 374 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO R 20 " -0.056 5.00e-02 4.00e+02 8.39e-02 1.13e+01 pdb=" N PRO R 21 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO R 21 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO R 21 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS R 297 " 0.047 5.00e-02 4.00e+02 7.21e-02 8.33e+00 pdb=" N PRO R 298 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO R 298 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO R 298 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG R 129 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.83e+00 pdb=" C ARG R 129 " -0.045 2.00e-02 2.50e+03 pdb=" O ARG R 129 " 0.017 2.00e-02 2.50e+03 pdb=" N PRO R 130 " 0.015 2.00e-02 2.50e+03 ... (remaining 371 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 571 2.81 - 3.33: 2032 3.33 - 3.86: 3502 3.86 - 4.38: 3706 4.38 - 4.90: 6530 Nonbonded interactions: 16341 Sorted by model distance: nonbonded pdb=" NH2 ARG R 91 " pdb=" O GLY R 155 " model vdw 2.290 3.120 nonbonded pdb=" O LEU R 209 " pdb=" NH1 ARG R 220 " model vdw 2.337 3.120 nonbonded pdb=" CE2 TYR R 77 " pdb=" ND1 HIS R 276 " model vdw 2.342 3.420 nonbonded pdb=" O GLY R 31 " pdb=" N ASN R 35 " model vdw 2.368 3.120 nonbonded pdb=" O ASP R 16 " pdb=" O TYR R 77 " model vdw 2.429 3.040 ... (remaining 16336 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: 1.360 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: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 2.610 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:0.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 4.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 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 : 0.006 0.084 2133 Z= 0.272 Angle : 0.948 9.575 2926 Z= 0.508 Chirality : 0.049 0.242 331 Planarity : 0.009 0.084 374 Dihedral : 13.233 62.594 700 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 0.54 % Allowed : 0.00 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.59 (0.49), residues: 284 helix: 0.65 (0.37), residues: 210 sheet: None (None), residues: 0 loop : -3.50 (0.52), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 160 TYR 0.014 0.002 TYR R 76 PHE 0.013 0.002 PHE R 93 TRP 0.010 0.002 TRP R 195 HIS 0.006 0.001 HIS R 276 Details of bonding type rmsd covalent geometry : bond 0.00618 ( 2132) covalent geometry : angle 0.94493 ( 2924) SS BOND : bond 0.00078 ( 1) SS BOND : angle 3.14123 ( 2) hydrogen bonds : bond 0.11775 ( 154) hydrogen bonds : angle 5.48062 ( 456) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.042 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 28 average time/residue: 0.0645 time to fit residues: 2.0248 Evaluate side-chains 25 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 27 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 1 optimal weight: 0.4980 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.1980 chunk 15 optimal weight: 0.1980 chunk 25 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 9 optimal weight: 0.3980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 45 GLN R 149 ASN R 159 HIS R 285 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.123589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.109008 restraints weight = 3154.321| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.56 r_work: 0.3343 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 2133 Z= 0.201 Angle : 0.791 7.517 2926 Z= 0.394 Chirality : 0.043 0.137 331 Planarity : 0.008 0.075 374 Dihedral : 5.490 22.494 317 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 1.09 % Allowed : 7.61 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.28 (0.49), residues: 284 helix: 1.03 (0.37), residues: 210 sheet: None (None), residues: 0 loop : -3.89 (0.46), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 224 TYR 0.013 0.001 TYR R 76 PHE 0.009 0.001 PHE R 93 TRP 0.010 0.001 TRP R 195 HIS 0.005 0.001 HIS R 276 Details of bonding type rmsd covalent geometry : bond 0.00488 ( 2132) covalent geometry : angle 0.78800 ( 2924) SS BOND : bond 0.00138 ( 1) SS BOND : angle 2.67710 ( 2) hydrogen bonds : bond 0.04380 ( 154) hydrogen bonds : angle 4.75190 ( 456) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.087 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 31 average time/residue: 0.1129 time to fit residues: 3.8607 Evaluate side-chains 32 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 236 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 19 optimal weight: 0.4980 chunk 20 optimal weight: 0.3980 chunk 16 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 22 optimal weight: 0.3980 chunk 23 optimal weight: 0.0870 chunk 5 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 25 optimal weight: 0.0170 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 149 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.124684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.110380 restraints weight = 3194.664| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.54 r_work: 0.3376 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2133 Z= 0.168 Angle : 0.708 6.471 2926 Z= 0.352 Chirality : 0.041 0.137 331 Planarity : 0.007 0.071 374 Dihedral : 5.105 22.138 317 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.09 % Allowed : 10.33 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 (0.51), residues: 284 helix: 1.35 (0.36), residues: 219 sheet: None (None), residues: 0 loop : -4.10 (0.47), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 224 TYR 0.009 0.001 TYR R 76 PHE 0.008 0.001 PHE R 107 TRP 0.008 0.001 TRP R 195 HIS 0.003 0.001 HIS R 276 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 2132) covalent geometry : angle 0.70588 ( 2924) SS BOND : bond 0.00124 ( 1) SS BOND : angle 2.14572 ( 2) hydrogen bonds : bond 0.03959 ( 154) hydrogen bonds : angle 4.58984 ( 456) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.075 Fit side-chains REVERT: R 112 SER cc_start: 0.8545 (t) cc_final: 0.8292 (p) outliers start: 2 outliers final: 1 residues processed: 36 average time/residue: 0.1013 time to fit residues: 4.0415 Evaluate side-chains 35 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 236 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 0.0980 chunk 26 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 1 optimal weight: 0.1980 chunk 20 optimal weight: 0.6980 chunk 22 optimal weight: 0.3980 chunk 9 optimal weight: 0.2980 overall best weight: 0.3180 ------------------------------------------------------------------------------- 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 = 0.3674 r_free = 0.3674 target = 0.125149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.110107 restraints weight = 3150.584| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.63 r_work: 0.3376 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 2133 Z= 0.175 Angle : 0.724 8.669 2926 Z= 0.354 Chirality : 0.041 0.137 331 Planarity : 0.007 0.069 374 Dihedral : 5.029 22.174 317 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.17 % Allowed : 11.41 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.26 (0.50), residues: 284 helix: 1.43 (0.37), residues: 213 sheet: None (None), residues: 0 loop : -3.94 (0.46), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 224 TYR 0.010 0.001 TYR R 76 PHE 0.008 0.001 PHE R 107 TRP 0.008 0.001 TRP R 195 HIS 0.002 0.001 HIS R 276 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 2132) covalent geometry : angle 0.72222 ( 2924) SS BOND : bond 0.00084 ( 1) SS BOND : angle 1.94251 ( 2) hydrogen bonds : bond 0.03989 ( 154) hydrogen bonds : angle 4.58517 ( 456) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.078 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 32 average time/residue: 0.0965 time to fit residues: 3.4700 Evaluate side-chains 34 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 GLN Chi-restraints excluded: chain R residue 169 TYR Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 236 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 4 optimal weight: 0.0980 chunk 23 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 17 optimal weight: 0.2980 chunk 15 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3658 r_free = 0.3658 target = 0.123638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.108335 restraints weight = 3088.789| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.67 r_work: 0.3348 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 2133 Z= 0.216 Angle : 0.747 7.482 2926 Z= 0.365 Chirality : 0.043 0.142 331 Planarity : 0.007 0.068 374 Dihedral : 5.104 22.248 317 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 2.72 % Allowed : 13.59 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.15 (0.50), residues: 284 helix: 1.34 (0.36), residues: 213 sheet: None (None), residues: 0 loop : -3.96 (0.46), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 220 TYR 0.013 0.001 TYR R 76 PHE 0.009 0.001 PHE R 97 TRP 0.009 0.002 TRP R 195 HIS 0.002 0.001 HIS R 276 Details of bonding type rmsd covalent geometry : bond 0.00523 ( 2132) covalent geometry : angle 0.74478 ( 2924) SS BOND : bond 0.00068 ( 1) SS BOND : angle 2.09070 ( 2) hydrogen bonds : bond 0.04286 ( 154) hydrogen bonds : angle 4.69344 ( 456) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.074 Fit side-chains REVERT: R 169 TYR cc_start: 0.8034 (OUTLIER) cc_final: 0.6728 (m-80) outliers start: 5 outliers final: 2 residues processed: 35 average time/residue: 0.0902 time to fit residues: 3.5611 Evaluate side-chains 35 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 GLN Chi-restraints excluded: chain R residue 169 TYR Chi-restraints excluded: chain R residue 236 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 8 optimal weight: 0.9980 chunk 4 optimal weight: 0.3980 chunk 25 optimal weight: 0.1980 chunk 7 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 chunk 11 optimal weight: 0.0170 chunk 10 optimal weight: 0.6980 chunk 21 optimal weight: 0.2980 chunk 16 optimal weight: 0.1980 chunk 27 optimal weight: 0.6980 chunk 24 optimal weight: 0.2980 overall best weight: 0.2018 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.126314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.111098 restraints weight = 3092.446| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.65 r_work: 0.3385 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2133 Z= 0.146 Angle : 0.684 7.342 2926 Z= 0.338 Chirality : 0.040 0.133 331 Planarity : 0.007 0.067 374 Dihedral : 4.840 22.200 317 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 1.63 % Allowed : 13.59 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.45 (0.51), residues: 284 helix: 1.56 (0.37), residues: 214 sheet: None (None), residues: 0 loop : -3.94 (0.46), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG R 224 TYR 0.010 0.001 TYR R 76 PHE 0.008 0.001 PHE R 97 TRP 0.007 0.001 TRP R 195 HIS 0.002 0.001 HIS R 276 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 2132) covalent geometry : angle 0.68302 ( 2924) SS BOND : bond 0.00121 ( 1) SS BOND : angle 1.73287 ( 2) hydrogen bonds : bond 0.03664 ( 154) hydrogen bonds : angle 4.49454 ( 456) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.072 Fit side-chains REVERT: R 169 TYR cc_start: 0.7976 (OUTLIER) cc_final: 0.6701 (m-80) REVERT: R 224 ARG cc_start: 0.7681 (ttt-90) cc_final: 0.7331 (ttt-90) outliers start: 3 outliers final: 0 residues processed: 33 average time/residue: 0.0940 time to fit residues: 3.4873 Evaluate side-chains 31 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 169 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 1 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 14 optimal weight: 0.0870 chunk 2 optimal weight: 0.9990 chunk 17 optimal weight: 0.0870 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 0.1980 chunk 5 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 overall best weight: 0.3336 ------------------------------------------------------------------------------- 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 = 0.3675 r_free = 0.3675 target = 0.124924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.109715 restraints weight = 3115.929| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.64 r_work: 0.3366 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 2133 Z= 0.176 Angle : 0.698 6.793 2926 Z= 0.347 Chirality : 0.041 0.136 331 Planarity : 0.007 0.065 374 Dihedral : 4.909 22.717 317 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 2.17 % Allowed : 13.04 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.39 (0.51), residues: 284 helix: 1.52 (0.37), residues: 214 sheet: None (None), residues: 0 loop : -3.97 (0.46), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG R 224 TYR 0.012 0.001 TYR R 76 PHE 0.009 0.001 PHE R 97 TRP 0.009 0.001 TRP R 195 HIS 0.002 0.001 HIS R 276 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 2132) covalent geometry : angle 0.69649 ( 2924) SS BOND : bond 0.00107 ( 1) SS BOND : angle 1.84830 ( 2) hydrogen bonds : bond 0.03920 ( 154) hydrogen bonds : angle 4.55282 ( 456) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.079 Fit side-chains REVERT: R 110 CYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8197 (m) REVERT: R 169 TYR cc_start: 0.7948 (OUTLIER) cc_final: 0.6736 (m-80) outliers start: 4 outliers final: 2 residues processed: 34 average time/residue: 0.0826 time to fit residues: 3.2040 Evaluate side-chains 36 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 GLN Chi-restraints excluded: chain R residue 110 CYS Chi-restraints excluded: chain R residue 169 TYR Chi-restraints excluded: chain R residue 181 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 3 optimal weight: 0.3980 chunk 14 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 20 optimal weight: 0.1980 chunk 0 optimal weight: 0.9990 chunk 9 optimal weight: 0.3980 chunk 22 optimal weight: 0.1980 chunk 5 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 27 optimal weight: 0.0050 chunk 4 optimal weight: 0.1980 overall best weight: 0.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 149 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.126771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.111668 restraints weight = 3079.812| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.64 r_work: 0.3395 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2133 Z= 0.142 Angle : 0.664 6.563 2926 Z= 0.331 Chirality : 0.040 0.134 331 Planarity : 0.007 0.065 374 Dihedral : 4.729 22.208 317 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 2.72 % Allowed : 13.04 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.72 (0.52), residues: 284 helix: 1.68 (0.37), residues: 219 sheet: None (None), residues: 0 loop : -3.99 (0.47), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG R 225 TYR 0.011 0.001 TYR R 76 PHE 0.009 0.001 PHE R 97 TRP 0.007 0.001 TRP R 195 HIS 0.002 0.001 HIS R 276 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 2132) covalent geometry : angle 0.66260 ( 2924) SS BOND : bond 0.00147 ( 1) SS BOND : angle 1.64954 ( 2) hydrogen bonds : bond 0.03533 ( 154) hydrogen bonds : angle 4.42342 ( 456) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.073 Fit side-chains REVERT: R 57 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7376 (tp) REVERT: R 169 TYR cc_start: 0.7969 (OUTLIER) cc_final: 0.6741 (m-80) REVERT: R 224 ARG cc_start: 0.7645 (ttt-90) cc_final: 0.7309 (ttt-90) outliers start: 5 outliers final: 2 residues processed: 37 average time/residue: 0.0982 time to fit residues: 4.0513 Evaluate side-chains 37 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 GLN Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 169 TYR Chi-restraints excluded: chain R residue 181 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 9 optimal weight: 0.0970 chunk 26 optimal weight: 0.9980 chunk 7 optimal weight: 0.0170 chunk 6 optimal weight: 0.5980 chunk 19 optimal weight: 0.2980 chunk 17 optimal weight: 0.9990 chunk 4 optimal weight: 0.1980 chunk 27 optimal weight: 0.0870 chunk 5 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 overall best weight: 0.1394 ------------------------------------------------------------------------------- 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 = 0.3721 r_free = 0.3721 target = 0.128489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.113364 restraints weight = 3142.910| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.68 r_work: 0.3413 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2133 Z= 0.136 Angle : 0.668 7.276 2926 Z= 0.337 Chirality : 0.039 0.157 331 Planarity : 0.007 0.065 374 Dihedral : 4.670 22.404 317 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.17 % Allowed : 15.22 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.79 (0.52), residues: 284 helix: 1.71 (0.36), residues: 221 sheet: None (None), residues: 0 loop : -4.03 (0.49), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 225 TYR 0.011 0.001 TYR R 76 PHE 0.008 0.001 PHE R 97 TRP 0.007 0.001 TRP R 195 HIS 0.009 0.001 HIS R 276 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 2132) covalent geometry : angle 0.66749 ( 2924) SS BOND : bond 0.00173 ( 1) SS BOND : angle 1.53277 ( 2) hydrogen bonds : bond 0.03414 ( 154) hydrogen bonds : angle 4.36101 ( 456) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.070 Fit side-chains REVERT: R 57 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7449 (tp) REVERT: R 169 TYR cc_start: 0.7956 (OUTLIER) cc_final: 0.6792 (m-80) REVERT: R 224 ARG cc_start: 0.7697 (ttt-90) cc_final: 0.7369 (ttt-90) outliers start: 4 outliers final: 2 residues processed: 35 average time/residue: 0.0877 time to fit residues: 3.4610 Evaluate side-chains 34 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 GLN Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 169 TYR Chi-restraints excluded: chain R residue 181 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 21 optimal weight: 0.0970 chunk 1 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 7 optimal weight: 0.1980 chunk 9 optimal weight: 0.0970 chunk 24 optimal weight: 0.4980 chunk 27 optimal weight: 0.4980 chunk 4 optimal weight: 0.1980 chunk 6 optimal weight: 0.0870 overall best weight: 0.1354 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.129440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.113955 restraints weight = 3117.943| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.77 r_work: 0.3419 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2133 Z= 0.138 Angle : 0.677 7.104 2926 Z= 0.339 Chirality : 0.039 0.145 331 Planarity : 0.007 0.065 374 Dihedral : 4.688 22.423 317 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 2.17 % Allowed : 15.76 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.83 (0.52), residues: 284 helix: 1.71 (0.36), residues: 221 sheet: None (None), residues: 0 loop : -3.92 (0.51), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 225 TYR 0.017 0.001 TYR R 275 PHE 0.008 0.001 PHE R 97 TRP 0.008 0.001 TRP R 195 HIS 0.010 0.002 HIS R 276 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 2132) covalent geometry : angle 0.67633 ( 2924) SS BOND : bond 0.00162 ( 1) SS BOND : angle 1.48852 ( 2) hydrogen bonds : bond 0.03405 ( 154) hydrogen bonds : angle 4.38103 ( 456) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.076 Fit side-chains REVERT: R 57 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7512 (tp) REVERT: R 169 TYR cc_start: 0.7963 (OUTLIER) cc_final: 0.6807 (m-80) REVERT: R 224 ARG cc_start: 0.7748 (ttt-90) cc_final: 0.7428 (ttt-90) outliers start: 4 outliers final: 2 residues processed: 35 average time/residue: 0.0966 time to fit residues: 3.8047 Evaluate side-chains 33 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 GLN Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 169 TYR Chi-restraints excluded: chain R residue 181 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 27 optimal weight: 0.0370 chunk 26 optimal weight: 0.5980 chunk 19 optimal weight: 0.0770 chunk 20 optimal weight: 0.0030 chunk 2 optimal weight: 0.0970 chunk 10 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 0.0970 chunk 5 optimal weight: 0.2980 chunk 8 optimal weight: 0.0970 chunk 25 optimal weight: 0.0000 overall best weight: 0.0428 ------------------------------------------------------------------------------- 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 = 0.3797 r_free = 0.3797 target = 0.134375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.120370 restraints weight = 3163.540| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.73 r_work: 0.3493 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2133 Z= 0.127 Angle : 0.661 7.184 2926 Z= 0.333 Chirality : 0.039 0.158 331 Planarity : 0.007 0.065 374 Dihedral : 4.489 22.454 317 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.17 % Allowed : 16.85 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.04 (0.52), residues: 284 helix: 1.90 (0.37), residues: 219 sheet: None (None), residues: 0 loop : -3.81 (0.51), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 225 TYR 0.014 0.001 TYR R 275 PHE 0.014 0.002 PHE R 125 TRP 0.009 0.001 TRP R 142 HIS 0.009 0.001 HIS R 276 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 2132) covalent geometry : angle 0.66026 ( 2924) SS BOND : bond 0.00176 ( 1) SS BOND : angle 1.26499 ( 2) hydrogen bonds : bond 0.02811 ( 154) hydrogen bonds : angle 4.20536 ( 456) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 893.55 seconds wall clock time: 17 minutes 6.03 seconds (1026.03 seconds total)