Starting phenix.real_space_refine on Tue Aug 4 11:44:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wmr_66102/08_2026/9wmr_66102.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wmr_66102/08_2026/9wmr_66102.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wmr_66102/08_2026/9wmr_66102.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wmr_66102/08_2026/9wmr_66102.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wmr_66102/08_2026/9wmr_66102.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wmr_66102/08_2026/9wmr_66102.map" } resolution = 2.48 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= 0.011 sd= 0.117 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 5 5.16 5 C 965 2.51 5 N 240 2.21 5 O 270 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 1480 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1480 Classifications: {'peptide': 182} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 169} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 0.73, per 1000 atoms: 0.49 Number of scatterers: 1480 At special positions: 0 Unit cell: (44, 75, 57, 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 5 16.00 O 270 8.00 N 240 7.00 C 965 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: 0.10 Conformation dependent library (CDL) restraints added in 59.3 milliseconds 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 346 Finding SS restraints... Secondary structure from input PDB file: 2 helices and 3 sheets defined 5.5% alpha, 52.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing helix chain 'A' and resid 68 through 72 removed outlier: 3.551A pdb=" N GLU A 71 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 99 Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 49 removed outlier: 3.830A pdb=" N LYS A 85 " --> pdb=" O TRP A 207 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ARG A 209 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE A 83 " --> pdb=" O ARG A 209 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 49 removed outlier: 3.830A pdb=" N LYS A 85 " --> pdb=" O TRP A 207 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ARG A 209 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE A 83 " --> pdb=" O ARG A 209 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 119 through 121 removed outlier: 3.507A pdb=" N THR A 119 " --> pdb=" O ALA A 62 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N THR A 67 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N GLY A 183 " --> pdb=" O THR A 67 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE A 104 " --> pdb=" O TYR A 190 " (cutoff:3.500A) 69 hydrogen bonds defined for protein. 174 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: 0.19 Time building geometry restraints manager: 0.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 221 1.31 - 1.43: 460 1.43 - 1.56: 841 1.56 - 1.68: 0 1.68 - 1.81: 10 Bond restraints: 1532 Sorted by residual: bond pdb=" C PRO A 59 " pdb=" O PRO A 59 " ideal model delta sigma weight residual 1.236 1.180 0.056 1.20e-02 6.94e+03 2.17e+01 bond pdb=" N VAL A 191 " pdb=" CA VAL A 191 " ideal model delta sigma weight residual 1.458 1.494 -0.036 7.70e-03 1.69e+04 2.16e+01 bond pdb=" C TRP A 60 " pdb=" O TRP A 60 " ideal model delta sigma weight residual 1.236 1.188 0.048 1.21e-02 6.83e+03 1.56e+01 bond pdb=" N SER A 212 " pdb=" CA SER A 212 " ideal model delta sigma weight residual 1.455 1.504 -0.049 1.25e-02 6.40e+03 1.51e+01 bond pdb=" C PRO A 96 " pdb=" O PRO A 96 " ideal model delta sigma weight residual 1.238 1.196 0.041 1.24e-02 6.50e+03 1.12e+01 ... (remaining 1527 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 1724 1.13 - 2.27: 268 2.27 - 3.40: 63 3.40 - 4.53: 30 4.53 - 5.67: 7 Bond angle restraints: 2092 Sorted by residual: angle pdb=" CA TYR A 210 " pdb=" C TYR A 210 " pdb=" O TYR A 210 " ideal model delta sigma weight residual 121.56 116.48 5.08 1.21e+00 6.83e-01 1.76e+01 angle pdb=" CA LYS A 211 " pdb=" C LYS A 211 " pdb=" N SER A 212 " ideal model delta sigma weight residual 118.39 124.06 -5.67 1.38e+00 5.25e-01 1.69e+01 angle pdb=" CA TRP A 172 " pdb=" C TRP A 172 " pdb=" O TRP A 172 " ideal model delta sigma weight residual 120.80 116.87 3.93 1.11e+00 8.12e-01 1.25e+01 angle pdb=" CA LYS A 211 " pdb=" C LYS A 211 " pdb=" O LYS A 211 " ideal model delta sigma weight residual 119.61 115.31 4.30 1.24e+00 6.50e-01 1.20e+01 angle pdb=" N PRO A 59 " pdb=" CA PRO A 59 " pdb=" CB PRO A 59 " ideal model delta sigma weight residual 102.33 98.26 4.07 1.18e+00 7.18e-01 1.19e+01 ... (remaining 2087 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.67: 826 12.67 - 25.34: 48 25.34 - 38.01: 13 38.01 - 50.68: 2 50.68 - 63.35: 1 Dihedral angle restraints: 890 sinusoidal: 352 harmonic: 538 Sorted by residual: dihedral pdb=" CA GLY A 183 " pdb=" C GLY A 183 " pdb=" N ALA A 184 " pdb=" CA ALA A 184 " ideal model delta harmonic sigma weight residual -180.00 -157.76 -22.24 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA LYS A 138 " pdb=" C LYS A 138 " pdb=" N LYS A 139 " pdb=" CA LYS A 139 " ideal model delta harmonic sigma weight residual -180.00 -158.18 -21.82 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA TRP A 182 " pdb=" C TRP A 182 " pdb=" N GLY A 183 " pdb=" CA GLY A 183 " ideal model delta harmonic sigma weight residual -180.00 -158.45 -21.55 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 887 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 126 0.044 - 0.088: 66 0.088 - 0.132: 24 0.132 - 0.176: 6 0.176 - 0.220: 4 Chirality restraints: 226 Sorted by residual: chirality pdb=" CA SER A 212 " pdb=" N SER A 212 " pdb=" C SER A 212 " pdb=" CB SER A 212 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CB ILE A 189 " pdb=" CA ILE A 189 " pdb=" CG1 ILE A 189 " pdb=" CG2 ILE A 189 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB VAL A 206 " pdb=" CA VAL A 206 " pdb=" CG1 VAL A 206 " pdb=" CG2 VAL A 206 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.85e-01 ... (remaining 223 not shown) Planarity restraints: 255 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 182 " -0.016 2.00e-02 2.50e+03 1.12e-02 3.13e+00 pdb=" CG TRP A 182 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP A 182 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP A 182 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 182 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 182 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 182 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 182 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 182 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 182 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 187 " -0.013 2.00e-02 2.50e+03 1.11e-02 3.10e+00 pdb=" CG TRP A 187 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP A 187 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 187 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 187 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 187 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 187 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 187 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 187 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 187 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 177 " -0.028 5.00e-02 4.00e+02 4.21e-02 2.83e+00 pdb=" N PRO A 178 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 178 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 178 " -0.023 5.00e-02 4.00e+02 ... (remaining 252 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 485 2.87 - 3.38: 1055 3.38 - 3.89: 2314 3.89 - 4.39: 2550 4.39 - 4.90: 4560 Nonbonded interactions: 10964 Sorted by model distance: nonbonded pdb=" O THR A 34 " pdb=" OG1 THR A 37 " model vdw 2.365 3.040 nonbonded pdb=" O THR A 37 " pdb=" O LYS A 211 " model vdw 2.413 3.040 nonbonded pdb=" OG1 THR A 154 " pdb=" O HIS A 158 " model vdw 2.467 3.040 nonbonded pdb=" OE1 GLU A 79 " pdb=" OG SER A 212 " model vdw 2.482 3.040 nonbonded pdb=" OD1 ASP A 177 " pdb=" OG1 THR A 179 " model vdw 2.556 3.040 ... (remaining 10959 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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.040 Find NCS groups from input model: 0.000 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 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 : 0.007 0.056 1532 Z= 0.459 Angle : 1.010 5.667 2092 Z= 0.633 Chirality : 0.065 0.220 226 Planarity : 0.006 0.042 255 Dihedral : 9.657 63.348 544 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.54), residues: 180 helix: None (None), residues: 0 sheet: -0.99 (0.54), residues: 81 loop : -1.98 (0.50), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 209 TYR 0.027 0.004 TYR A 201 PHE 0.014 0.003 PHE A 145 TRP 0.029 0.004 TRP A 187 HIS 0.007 0.002 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00709 / 0.46 ( 1532) covalent geometry : angle 1.00999 / 0.63 ( 2092) hydrogen bonds : bond 0.28091 / 18.63 ( 50) hydrogen bonds : angle 8.98512 / 6.07 ( 174) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.060 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.5667 time to fit residues: 19.5857 Evaluate side-chains 24 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 12 optimal weight: 20.0000 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 11 optimal weight: 0.0980 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.114109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.101556 restraints weight = 1825.226| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.31 r_work: 0.3052 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 1532 Z= 0.133 Angle : 0.615 6.134 2092 Z= 0.344 Chirality : 0.047 0.119 226 Planarity : 0.005 0.035 255 Dihedral : 5.494 18.514 197 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.23 % Allowed : 6.17 % Favored : 92.59 % 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: -1.58 (0.56), residues: 180 helix: None (None), residues: 0 sheet: -0.29 (0.54), residues: 81 loop : -1.75 (0.53), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 132 TYR 0.009 0.002 TYR A 43 PHE 0.005 0.001 PHE A 65 TRP 0.011 0.001 TRP A 172 HIS 0.003 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 ( 1532) covalent geometry : angle 0.61525 / 0.34 ( 2092) hydrogen bonds : bond 0.04584 / 3.14 ( 50) hydrogen bonds : angle 5.38039 / 3.45 ( 174) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.066 Fit side-chains REVERT: A 100 LYS cc_start: 0.8554 (mtmm) cc_final: 0.8228 (mmtm) outliers start: 2 outliers final: 0 residues processed: 22 average time/residue: 0.5969 time to fit residues: 13.3783 Evaluate side-chains 20 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 9 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 chunk 13 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 8 optimal weight: 20.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.109332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.096574 restraints weight = 1833.912| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.33 r_work: 0.2992 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 1532 Z= 0.192 Angle : 0.695 5.522 2092 Z= 0.393 Chirality : 0.051 0.138 226 Planarity : 0.006 0.039 255 Dihedral : 5.853 20.284 197 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.23 % Allowed : 8.02 % Favored : 90.74 % 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: -1.33 (0.56), residues: 180 helix: None (None), residues: 0 sheet: -0.05 (0.54), residues: 81 loop : -1.66 (0.54), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 143 TYR 0.016 0.002 TYR A 43 PHE 0.007 0.002 PHE A 65 TRP 0.012 0.002 TRP A 172 HIS 0.004 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 ( 1532) covalent geometry : angle 0.69479 / 0.39 ( 2092) hydrogen bonds : bond 0.05092 / 3.53 ( 50) hydrogen bonds : angle 5.29078 / 3.40 ( 174) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.061 Fit side-chains REVERT: A 100 LYS cc_start: 0.8520 (mtmm) cc_final: 0.8166 (mmtm) outliers start: 2 outliers final: 0 residues processed: 21 average time/residue: 0.5566 time to fit residues: 11.9060 Evaluate side-chains 19 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 4 optimal weight: 8.9990 chunk 16 optimal weight: 8.9990 chunk 13 optimal weight: 0.0870 chunk 7 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 overall best weight: 3.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.110223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.097398 restraints weight = 1884.052| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.34 r_work: 0.3003 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 1532 Z= 0.164 Angle : 0.653 5.638 2092 Z= 0.367 Chirality : 0.049 0.119 226 Planarity : 0.006 0.035 255 Dihedral : 5.648 19.396 197 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.62 % Allowed : 9.88 % Favored : 89.51 % 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: -1.24 (0.56), residues: 180 helix: None (None), residues: 0 sheet: 0.02 (0.53), residues: 81 loop : -1.60 (0.54), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 68 TYR 0.014 0.002 TYR A 43 PHE 0.007 0.001 PHE A 65 TRP 0.011 0.001 TRP A 172 HIS 0.003 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 ( 1532) covalent geometry : angle 0.65266 / 0.37 ( 2092) hydrogen bonds : bond 0.04638 / 3.23 ( 50) hydrogen bonds : angle 5.10575 / 3.27 ( 174) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.063 Fit side-chains REVERT: A 100 LYS cc_start: 0.8508 (mtmm) cc_final: 0.8156 (mmtm) REVERT: A 177 ASP cc_start: 0.9175 (t0) cc_final: 0.8960 (t0) outliers start: 1 outliers final: 1 residues processed: 23 average time/residue: 0.5381 time to fit residues: 12.6118 Evaluate side-chains 22 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 21 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 1 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.110885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.098107 restraints weight = 1836.787| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.34 r_work: 0.2997 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 1532 Z= 0.146 Angle : 0.620 5.587 2092 Z= 0.346 Chirality : 0.048 0.119 226 Planarity : 0.006 0.035 255 Dihedral : 5.418 18.672 197 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 10.49 % Favored : 89.51 % 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: -1.09 (0.57), residues: 180 helix: None (None), residues: 0 sheet: 0.09 (0.54), residues: 81 loop : -1.46 (0.57), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 68 TYR 0.012 0.002 TYR A 43 PHE 0.007 0.001 PHE A 104 TRP 0.009 0.001 TRP A 172 HIS 0.003 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 ( 1532) covalent geometry : angle 0.61976 / 0.35 ( 2092) hydrogen bonds : bond 0.04318 / 3.01 ( 50) hydrogen bonds : angle 4.96393 / 3.18 ( 174) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.057 Fit side-chains REVERT: A 100 LYS cc_start: 0.8522 (mtmm) cc_final: 0.8149 (mmtm) REVERT: A 177 ASP cc_start: 0.9179 (t0) cc_final: 0.8967 (t0) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.5626 time to fit residues: 12.0288 Evaluate side-chains 21 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.107608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.094773 restraints weight = 1843.743| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.34 r_work: 0.2959 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 1532 Z= 0.234 Angle : 0.759 6.418 2092 Z= 0.427 Chirality : 0.053 0.139 226 Planarity : 0.007 0.046 255 Dihedral : 6.084 22.101 197 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.62 % Allowed : 9.88 % Favored : 89.51 % 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: -1.19 (0.56), residues: 180 helix: None (None), residues: 0 sheet: 0.03 (0.54), residues: 81 loop : -1.54 (0.54), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 143 TYR 0.017 0.002 TYR A 43 PHE 0.008 0.002 PHE A 65 TRP 0.011 0.002 TRP A 172 HIS 0.005 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.23 ( 1532) covalent geometry : angle 0.75860 / 0.43 ( 2092) hydrogen bonds : bond 0.05337 / 3.71 ( 50) hydrogen bonds : angle 5.23748 / 3.38 ( 174) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 21 time to evaluate : 0.060 Fit side-chains REVERT: A 118 ASN cc_start: 0.9276 (t0) cc_final: 0.8982 (t0) outliers start: 1 outliers final: 1 residues processed: 22 average time/residue: 0.6250 time to fit residues: 13.9861 Evaluate side-chains 22 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 21 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.110059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.097338 restraints weight = 1848.026| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.33 r_work: 0.3012 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1532 Z= 0.152 Angle : 0.641 5.949 2092 Z= 0.356 Chirality : 0.048 0.120 226 Planarity : 0.006 0.039 255 Dihedral : 5.523 19.122 197 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.62 % Allowed : 9.88 % Favored : 89.51 % 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: -1.06 (0.57), residues: 180 helix: None (None), residues: 0 sheet: 0.04 (0.53), residues: 81 loop : -1.37 (0.56), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 143 TYR 0.012 0.002 TYR A 43 PHE 0.008 0.001 PHE A 104 TRP 0.009 0.001 TRP A 172 HIS 0.003 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 ( 1532) covalent geometry : angle 0.64083 / 0.36 ( 2092) hydrogen bonds : bond 0.04394 / 3.07 ( 50) hydrogen bonds : angle 4.97947 / 3.19 ( 174) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 21 time to evaluate : 0.071 Fit side-chains REVERT: A 100 LYS cc_start: 0.8509 (mtmm) cc_final: 0.8167 (mmtm) REVERT: A 177 ASP cc_start: 0.9180 (t0) cc_final: 0.8963 (t0) outliers start: 1 outliers final: 0 residues processed: 21 average time/residue: 0.6054 time to fit residues: 12.9449 Evaluate side-chains 21 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 2 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 chunk 9 optimal weight: 0.0470 chunk 15 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 overall best weight: 2.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.112027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.099447 restraints weight = 1832.247| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.33 r_work: 0.3021 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 1532 Z= 0.125 Angle : 0.604 7.566 2092 Z= 0.329 Chirality : 0.046 0.121 226 Planarity : 0.005 0.036 255 Dihedral : 5.080 17.360 197 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.00 % Allowed : 10.49 % Favored : 89.51 % 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: -0.92 (0.58), residues: 180 helix: None (None), residues: 0 sheet: 0.09 (0.53), residues: 81 loop : -1.23 (0.58), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 132 TYR 0.011 0.001 TYR A 144 PHE 0.008 0.001 PHE A 104 TRP 0.007 0.001 TRP A 172 HIS 0.002 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 1532) covalent geometry : angle 0.60430 / 0.33 ( 2092) hydrogen bonds : bond 0.03920 / 2.74 ( 50) hydrogen bonds : angle 4.80073 / 3.07 ( 174) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.064 Fit side-chains REVERT: A 100 LYS cc_start: 0.8483 (mtmm) cc_final: 0.8140 (mmtm) REVERT: A 177 ASP cc_start: 0.9180 (t0) cc_final: 0.8966 (t0) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.5238 time to fit residues: 12.7985 Evaluate side-chains 21 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 17 optimal weight: 9.9990 chunk 8 optimal weight: 20.0000 chunk 16 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 11 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.110029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.097145 restraints weight = 1849.527| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.35 r_work: 0.2999 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 1532 Z= 0.166 Angle : 0.667 8.518 2092 Z= 0.371 Chirality : 0.049 0.142 226 Planarity : 0.008 0.095 255 Dihedral : 5.487 19.093 197 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 10.49 % Favored : 89.51 % 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: -0.96 (0.57), residues: 180 helix: None (None), residues: 0 sheet: 0.05 (0.53), residues: 81 loop : -1.23 (0.57), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 68 TYR 0.013 0.002 TYR A 43 PHE 0.008 0.001 PHE A 104 TRP 0.008 0.001 TRP A 207 HIS 0.004 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 ( 1532) covalent geometry : angle 0.66671 / 0.37 ( 2092) hydrogen bonds : bond 0.04411 / 3.09 ( 50) hydrogen bonds : angle 4.94852 / 3.18 ( 174) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.068 Fit side-chains REVERT: A 100 LYS cc_start: 0.8488 (mtmm) cc_final: 0.8130 (mmtm) REVERT: A 177 ASP cc_start: 0.9178 (t0) cc_final: 0.8960 (t0) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.5891 time to fit residues: 13.1932 Evaluate side-chains 21 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 2 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 10 optimal weight: 0.0870 chunk 4 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.113681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.101228 restraints weight = 1858.198| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.32 r_work: 0.3071 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 1532 Z= 0.113 Angle : 0.573 8.285 2092 Z= 0.312 Chirality : 0.045 0.121 226 Planarity : 0.007 0.082 255 Dihedral : 4.792 16.438 197 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.00 % Allowed : 10.49 % Favored : 89.51 % 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: -0.82 (0.58), residues: 180 helix: None (None), residues: 0 sheet: 0.25 (0.53), residues: 79 loop : -1.22 (0.59), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 68 TYR 0.010 0.001 TYR A 144 PHE 0.009 0.001 PHE A 104 TRP 0.005 0.001 TRP A 172 HIS 0.002 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 1532) covalent geometry : angle 0.57317 / 0.31 ( 2092) hydrogen bonds : bond 0.03575 / 2.50 ( 50) hydrogen bonds : angle 4.66585 / 2.98 ( 174) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.062 Fit side-chains REVERT: A 100 LYS cc_start: 0.8436 (mtmm) cc_final: 0.8073 (mmtm) REVERT: A 177 ASP cc_start: 0.9181 (t0) cc_final: 0.8974 (t0) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.4545 time to fit residues: 10.2289 Evaluate side-chains 22 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 8 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.110252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.097551 restraints weight = 1815.543| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.32 r_work: 0.3019 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 1532 Z= 0.167 Angle : 0.676 9.916 2092 Z= 0.372 Chirality : 0.049 0.134 226 Planarity : 0.008 0.082 255 Dihedral : 5.394 18.808 197 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 10.49 % Favored : 89.51 % 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: -0.86 (0.58), residues: 180 helix: None (None), residues: 0 sheet: 0.08 (0.53), residues: 81 loop : -1.14 (0.58), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 68 TYR 0.012 0.002 TYR A 43 PHE 0.008 0.001 PHE A 104 TRP 0.008 0.001 TRP A 207 HIS 0.003 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 ( 1532) covalent geometry : angle 0.67561 / 0.37 ( 2092) hydrogen bonds : bond 0.04357 / 3.05 ( 50) hydrogen bonds : angle 4.91143 / 3.15 ( 174) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 821.83 seconds wall clock time: 14 minutes 55.40 seconds (895.40 seconds total)