Starting phenix.real_space_refine on Tue Feb 3 12:38:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lrz_63348/02_2026/9lrz_63348.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lrz_63348/02_2026/9lrz_63348.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lrz_63348/02_2026/9lrz_63348.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lrz_63348/02_2026/9lrz_63348.map" model { file = "/net/cci-nas-00/data/ceres_data/9lrz_63348/02_2026/9lrz_63348.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lrz_63348/02_2026/9lrz_63348.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 1324 2.51 5 N 405 2.21 5 O 430 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2172 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2172 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 2, 'TRANS': 277} Time building chain proxies: 0.63, per 1000 atoms: 0.29 Number of scatterers: 2172 At special positions: 0 Unit cell: (48.59, 68.93, 152.55, 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 430 8.00 N 405 7.00 C 1324 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: 0.16 Conformation dependent library (CDL) restraints added in 81.3 milliseconds 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 526 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 2 sheets defined 72.9% alpha, 2.9% 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 6 through 33 Processing helix chain 'A' and resid 42 through 98 removed outlier: 3.977A pdb=" N GLU A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER A 83 " --> pdb=" O PHE A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 128 removed outlier: 3.680A pdb=" N GLU A 113 " --> pdb=" O MET A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 242 removed outlier: 4.190A pdb=" N GLY A 196 " --> pdb=" O ASN A 192 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR A 197 " --> pdb=" O ASP A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 271 removed outlier: 3.611A pdb=" N VAL A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 280 removed outlier: 3.561A pdb=" N SER A 278 " --> pdb=" O GLY A 275 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 129 through 130 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 152 removed outlier: 4.305A pdb=" N MET A 149 " --> pdb=" O VAL A 163 " (cutoff:3.500A) 179 hydrogen bonds defined for protein. 519 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: 0.22 Time building geometry restraints manager: 0.22 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: 780 1.34 - 1.46: 341 1.46 - 1.58: 1044 1.58 - 1.70: 0 1.70 - 1.82: 26 Bond restraints: 2191 Sorted by residual: bond pdb=" N ASN A 211 " pdb=" CA ASN A 211 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.19e-02 7.06e+03 5.94e+00 bond pdb=" N PHE A 216 " pdb=" CA PHE A 216 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.19e-02 7.06e+03 5.91e+00 bond pdb=" N ARG A 171 " pdb=" CA ARG A 171 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.24e-02 6.50e+03 5.88e+00 bond pdb=" N TYR A 215 " pdb=" CA TYR A 215 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.19e-02 7.06e+03 5.76e+00 bond pdb=" N ASN A 217 " pdb=" CA ASN A 217 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.19e-02 7.06e+03 5.68e+00 ... (remaining 2186 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 2881 1.55 - 3.10: 50 3.10 - 4.65: 11 4.65 - 6.20: 1 6.20 - 7.75: 1 Bond angle restraints: 2944 Sorted by residual: angle pdb=" N THR A 169 " pdb=" CA THR A 169 " pdb=" C THR A 169 " ideal model delta sigma weight residual 110.59 104.47 6.12 1.45e+00 4.76e-01 1.78e+01 angle pdb=" CA THR A 169 " pdb=" C THR A 169 " pdb=" O THR A 169 " ideal model delta sigma weight residual 121.89 117.44 4.45 1.17e+00 7.31e-01 1.45e+01 angle pdb=" CA ARG A 171 " pdb=" C ARG A 171 " pdb=" O ARG A 171 " ideal model delta sigma weight residual 120.55 117.08 3.47 1.07e+00 8.73e-01 1.05e+01 angle pdb=" N ALA A 170 " pdb=" CA ALA A 170 " pdb=" C ALA A 170 " ideal model delta sigma weight residual 113.01 109.65 3.36 1.20e+00 6.94e-01 7.82e+00 angle pdb=" CA THR A 169 " pdb=" C THR A 169 " pdb=" N ALA A 170 " ideal model delta sigma weight residual 115.36 119.10 -3.74 1.37e+00 5.33e-01 7.47e+00 ... (remaining 2939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.26: 1147 17.26 - 34.51: 139 34.51 - 51.77: 57 51.77 - 69.03: 10 69.03 - 86.29: 9 Dihedral angle restraints: 1362 sinusoidal: 554 harmonic: 808 Sorted by residual: dihedral pdb=" CA ASN A 156 " pdb=" C ASN A 156 " pdb=" N MET A 157 " pdb=" CA MET A 157 " ideal model delta harmonic sigma weight residual -180.00 -156.69 -23.31 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CG ARG A 53 " pdb=" CD ARG A 53 " pdb=" NE ARG A 53 " pdb=" CZ ARG A 53 " ideal model delta sinusoidal sigma weight residual -180.00 -136.65 -43.35 2 1.50e+01 4.44e-03 1.01e+01 dihedral pdb=" CB MET A 70 " pdb=" CG MET A 70 " pdb=" SD MET A 70 " pdb=" CE MET A 70 " ideal model delta sinusoidal sigma weight residual 60.00 119.44 -59.44 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 1359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 218 0.034 - 0.068: 88 0.068 - 0.102: 22 0.102 - 0.136: 7 0.136 - 0.170: 1 Chirality restraints: 336 Sorted by residual: chirality pdb=" CA MET A 168 " pdb=" N MET A 168 " pdb=" C MET A 168 " pdb=" CB MET A 168 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.26e-01 chirality pdb=" CA LEU A 212 " pdb=" N LEU A 212 " pdb=" C LEU A 212 " pdb=" CB LEU A 212 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.15e-01 chirality pdb=" CA VAL A 163 " pdb=" N VAL A 163 " pdb=" C VAL A 163 " pdb=" CB VAL A 163 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.43e-01 ... (remaining 333 not shown) Planarity restraints: 393 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 168 " -0.007 2.00e-02 2.50e+03 1.47e-02 2.15e+00 pdb=" C MET A 168 " 0.025 2.00e-02 2.50e+03 pdb=" O MET A 168 " -0.009 2.00e-02 2.50e+03 pdb=" N THR A 169 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 18 " 0.012 2.00e-02 2.50e+03 9.83e-03 1.69e+00 pdb=" CG PHE A 18 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE A 18 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 18 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 18 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 18 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 18 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 18 " 0.005 2.00e-02 2.50e+03 1.07e-02 1.15e+00 pdb=" C PHE A 18 " -0.019 2.00e-02 2.50e+03 pdb=" O PHE A 18 " 0.007 2.00e-02 2.50e+03 pdb=" N GLN A 19 " 0.006 2.00e-02 2.50e+03 ... (remaining 390 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 749 2.87 - 3.38: 2217 3.38 - 3.89: 3709 3.89 - 4.39: 3903 4.39 - 4.90: 6597 Nonbonded interactions: 17175 Sorted by model distance: nonbonded pdb=" O THR A 167 " pdb=" NH1 ARG A 204 " model vdw 2.365 3.120 nonbonded pdb=" OE2 GLU A 120 " pdb=" NH2 ARG A 123 " model vdw 2.372 3.120 nonbonded pdb=" O THR A 187 " pdb=" OG SER A 191 " model vdw 2.380 3.040 nonbonded pdb=" N GLU A 181 " pdb=" OE1 GLU A 181 " model vdw 2.418 3.120 nonbonded pdb=" O ALA A 246 " pdb=" OG1 THR A 249 " model vdw 2.496 3.040 ... (remaining 17170 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: 2.560 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: 0.000 Set scattering table: 0.010 Process input model: 3.490 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:5.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2191 Z= 0.253 Angle : 0.561 7.750 2944 Z= 0.365 Chirality : 0.040 0.170 336 Planarity : 0.004 0.026 393 Dihedral : 19.202 86.287 836 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.85 % Allowed : 21.37 % Favored : 77.78 % 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: 3.16 (0.49), residues: 278 helix: 3.18 (0.35), residues: 204 sheet: None (None), residues: 0 loop : -1.28 (0.57), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 14 TYR 0.003 0.001 TYR A 215 PHE 0.022 0.002 PHE A 18 TRP 0.002 0.001 TRP A 150 HIS 0.004 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 2191) covalent geometry : angle 0.56136 ( 2944) hydrogen bonds : bond 0.11975 ( 179) hydrogen bonds : angle 4.04363 ( 519) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.052 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 49 average time/residue: 0.5183 time to fit residues: 25.7929 Evaluate side-chains 45 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 27 optimal weight: 0.0980 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 25 optimal weight: 0.4980 chunk 26 optimal weight: 0.5980 chunk 9 optimal weight: 0.0970 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 99 ASN A 134 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.121219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.109134 restraints weight = 2339.216| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 0.94 r_work: 0.3079 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 2.23 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.0509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2191 Z= 0.172 Angle : 0.457 4.948 2944 Z= 0.263 Chirality : 0.036 0.112 336 Planarity : 0.003 0.028 393 Dihedral : 4.774 42.163 305 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 2.99 % Allowed : 20.09 % Favored : 76.92 % 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: 3.33 (0.49), residues: 278 helix: 3.31 (0.34), residues: 204 sheet: None (None), residues: 0 loop : -1.20 (0.58), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 107 TYR 0.003 0.001 TYR A 230 PHE 0.020 0.002 PHE A 18 TRP 0.003 0.001 TRP A 150 HIS 0.005 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 2191) covalent geometry : angle 0.45651 ( 2944) hydrogen bonds : bond 0.07498 ( 179) hydrogen bonds : angle 3.55931 ( 519) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.089 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 49 average time/residue: 0.6254 time to fit residues: 31.1452 Evaluate side-chains 46 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 171 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 4 optimal weight: 0.1980 chunk 11 optimal weight: 0.2980 chunk 25 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 21 optimal weight: 0.0980 chunk 27 optimal weight: 0.0870 chunk 1 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 0.2980 chunk 6 optimal weight: 0.5980 overall best weight: 0.1958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 57 ASN A 99 ASN A 134 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.123175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.110913 restraints weight = 2312.211| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 0.95 r_work: 0.3153 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 2.23 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.0848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2191 Z= 0.131 Angle : 0.404 5.128 2944 Z= 0.231 Chirality : 0.034 0.115 336 Planarity : 0.002 0.028 393 Dihedral : 4.470 38.866 305 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 2.99 % Allowed : 19.66 % Favored : 77.35 % 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: 3.74 (0.49), residues: 278 helix: 3.64 (0.34), residues: 204 sheet: None (None), residues: 0 loop : -1.15 (0.59), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 218 TYR 0.003 0.001 TYR A 215 PHE 0.011 0.001 PHE A 18 TRP 0.003 0.001 TRP A 150 HIS 0.002 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 2191) covalent geometry : angle 0.40392 ( 2944) hydrogen bonds : bond 0.06312 ( 179) hydrogen bonds : angle 3.30907 ( 519) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.088 Fit side-chains REVERT: A 3 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8813 (pp) REVERT: A 4 ASN cc_start: 0.8585 (t0) cc_final: 0.8359 (t0) outliers start: 7 outliers final: 2 residues processed: 50 average time/residue: 0.6614 time to fit residues: 33.6134 Evaluate side-chains 48 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 171 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 25 optimal weight: 0.3980 chunk 19 optimal weight: 0.3980 chunk 5 optimal weight: 0.9990 chunk 10 optimal weight: 0.4980 chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 6 optimal weight: 0.3980 chunk 1 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 99 ASN A 134 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.119913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.107612 restraints weight = 2296.452| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 0.95 r_work: 0.3066 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.0667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2191 Z= 0.190 Angle : 0.484 5.734 2944 Z= 0.277 Chirality : 0.037 0.111 336 Planarity : 0.003 0.027 393 Dihedral : 4.827 43.023 305 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 2.99 % Allowed : 20.09 % Favored : 76.92 % 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: 3.27 (0.48), residues: 278 helix: 3.26 (0.34), residues: 204 sheet: None (None), residues: 0 loop : -1.20 (0.58), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 14 TYR 0.004 0.001 TYR A 102 PHE 0.022 0.002 PHE A 18 TRP 0.003 0.001 TRP A 150 HIS 0.005 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 2191) covalent geometry : angle 0.48445 ( 2944) hydrogen bonds : bond 0.07781 ( 179) hydrogen bonds : angle 3.58453 ( 519) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.089 Fit side-chains REVERT: A 3 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8791 (pp) outliers start: 7 outliers final: 4 residues processed: 49 average time/residue: 0.7215 time to fit residues: 35.9108 Evaluate side-chains 52 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 171 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 8 optimal weight: 0.7980 chunk 13 optimal weight: 0.4980 chunk 5 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 22 optimal weight: 0.0970 chunk 16 optimal weight: 0.9990 chunk 27 optimal weight: 0.1980 chunk 23 optimal weight: 0.3980 chunk 24 optimal weight: 0.0870 chunk 6 optimal weight: 0.3980 chunk 9 optimal weight: 0.2980 overall best weight: 0.2156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 134 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.122926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.110683 restraints weight = 2336.651| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 0.95 r_work: 0.3111 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2191 Z= 0.135 Angle : 0.423 5.837 2944 Z= 0.240 Chirality : 0.034 0.114 336 Planarity : 0.003 0.027 393 Dihedral : 4.514 39.624 305 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 2.56 % Allowed : 20.51 % Favored : 76.92 % 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: 3.68 (0.49), residues: 278 helix: 3.60 (0.33), residues: 204 sheet: None (None), residues: 0 loop : -1.20 (0.59), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 107 TYR 0.004 0.001 TYR A 215 PHE 0.012 0.001 PHE A 18 TRP 0.003 0.001 TRP A 150 HIS 0.002 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 2191) covalent geometry : angle 0.42284 ( 2944) hydrogen bonds : bond 0.06398 ( 179) hydrogen bonds : angle 3.33051 ( 519) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.090 Fit side-chains REVERT: A 3 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8774 (pp) REVERT: A 4 ASN cc_start: 0.8616 (t0) cc_final: 0.8374 (t0) REVERT: A 182 LEU cc_start: 0.9025 (mp) cc_final: 0.8802 (mp) outliers start: 6 outliers final: 3 residues processed: 51 average time/residue: 0.6152 time to fit residues: 31.8941 Evaluate side-chains 49 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 171 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 8 optimal weight: 0.5980 chunk 14 optimal weight: 0.0030 chunk 15 optimal weight: 0.1980 chunk 25 optimal weight: 0.3980 chunk 7 optimal weight: 0.4980 chunk 21 optimal weight: 0.1980 chunk 19 optimal weight: 0.2980 chunk 17 optimal weight: 0.7980 chunk 13 optimal weight: 0.4980 chunk 9 optimal weight: 0.3980 chunk 3 optimal weight: 0.9990 overall best weight: 0.2190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 134 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.125252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.112759 restraints weight = 2299.536| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.01 r_work: 0.3107 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2191 Z= 0.136 Angle : 0.430 6.029 2944 Z= 0.243 Chirality : 0.034 0.113 336 Planarity : 0.002 0.027 393 Dihedral : 4.481 38.795 305 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 2.99 % Allowed : 19.66 % Favored : 77.35 % 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: 3.69 (0.49), residues: 278 helix: 3.61 (0.33), residues: 204 sheet: None (None), residues: 0 loop : -1.21 (0.59), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 107 TYR 0.003 0.001 TYR A 215 PHE 0.013 0.002 PHE A 18 TRP 0.003 0.001 TRP A 150 HIS 0.002 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 2191) covalent geometry : angle 0.43038 ( 2944) hydrogen bonds : bond 0.06437 ( 179) hydrogen bonds : angle 3.31236 ( 519) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.055 Fit side-chains REVERT: A 3 ILE cc_start: 0.9026 (OUTLIER) cc_final: 0.8745 (pp) REVERT: A 182 LEU cc_start: 0.9022 (mp) cc_final: 0.8819 (mp) outliers start: 7 outliers final: 3 residues processed: 52 average time/residue: 0.5209 time to fit residues: 27.5712 Evaluate side-chains 49 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 171 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 16 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 24 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 22 optimal weight: 0.0870 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 0.2980 chunk 15 optimal weight: 0.3980 chunk 27 optimal weight: 0.0030 chunk 6 optimal weight: 0.0980 overall best weight: 0.1768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 134 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.124869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.112627 restraints weight = 2324.793| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 0.93 r_work: 0.3142 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 2.25 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 2191 Z= 0.127 Angle : 0.426 6.655 2944 Z= 0.237 Chirality : 0.033 0.115 336 Planarity : 0.002 0.027 393 Dihedral : 4.344 36.426 305 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 2.14 % Allowed : 22.22 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.83 (0.49), residues: 278 helix: 3.72 (0.33), residues: 204 sheet: None (None), residues: 0 loop : -1.18 (0.59), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 209 TYR 0.003 0.001 TYR A 215 PHE 0.010 0.001 PHE A 18 TRP 0.003 0.001 TRP A 150 HIS 0.002 0.001 HIS A 158 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 2191) covalent geometry : angle 0.42585 ( 2944) hydrogen bonds : bond 0.06052 ( 179) hydrogen bonds : angle 3.23367 ( 519) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.087 Fit side-chains REVERT: A 3 ILE cc_start: 0.9078 (OUTLIER) cc_final: 0.8833 (pp) REVERT: A 182 LEU cc_start: 0.9016 (mp) cc_final: 0.8802 (mp) outliers start: 5 outliers final: 2 residues processed: 49 average time/residue: 0.5037 time to fit residues: 25.1397 Evaluate side-chains 48 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 171 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 9 optimal weight: 0.3980 chunk 14 optimal weight: 0.0010 chunk 19 optimal weight: 0.5980 chunk 15 optimal weight: 0.0470 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 0.0970 chunk 1 optimal weight: 0.9990 chunk 25 optimal weight: 0.3980 chunk 7 optimal weight: 0.5980 overall best weight: 0.1882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 134 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.123861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.111468 restraints weight = 2302.179| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 0.96 r_work: 0.3129 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 2191 Z= 0.130 Angle : 0.437 6.895 2944 Z= 0.242 Chirality : 0.033 0.115 336 Planarity : 0.002 0.027 393 Dihedral : 4.344 36.283 305 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 2.14 % Allowed : 22.22 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.80 (0.48), residues: 278 helix: 3.69 (0.33), residues: 204 sheet: None (None), residues: 0 loop : -1.17 (0.59), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 209 TYR 0.003 0.001 TYR A 215 PHE 0.011 0.001 PHE A 18 TRP 0.002 0.001 TRP A 150 HIS 0.002 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 2191) covalent geometry : angle 0.43697 ( 2944) hydrogen bonds : bond 0.06117 ( 179) hydrogen bonds : angle 3.23422 ( 519) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.092 Fit side-chains REVERT: A 3 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8789 (pp) REVERT: A 182 LEU cc_start: 0.9034 (mp) cc_final: 0.8827 (mp) outliers start: 5 outliers final: 4 residues processed: 48 average time/residue: 0.6503 time to fit residues: 31.7354 Evaluate side-chains 50 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 189 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 11 optimal weight: 0.3980 chunk 23 optimal weight: 0.2980 chunk 18 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 10 optimal weight: 0.0670 chunk 4 optimal weight: 0.5980 chunk 19 optimal weight: 0.4980 chunk 24 optimal weight: 0.6980 chunk 2 optimal weight: 0.2980 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 overall best weight: 0.2918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 134 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.121553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.109136 restraints weight = 2337.509| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 0.96 r_work: 0.3105 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2191 Z= 0.154 Angle : 0.474 7.549 2944 Z= 0.263 Chirality : 0.035 0.113 336 Planarity : 0.003 0.027 393 Dihedral : 4.566 39.244 305 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 2.56 % Allowed : 22.22 % Favored : 75.21 % 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: 3.52 (0.48), residues: 278 helix: 3.47 (0.33), residues: 204 sheet: None (None), residues: 0 loop : -1.20 (0.58), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 209 TYR 0.003 0.001 TYR A 215 PHE 0.017 0.002 PHE A 18 TRP 0.002 0.001 TRP A 150 HIS 0.003 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 2191) covalent geometry : angle 0.47397 ( 2944) hydrogen bonds : bond 0.06896 ( 179) hydrogen bonds : angle 3.37787 ( 519) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.066 Fit side-chains REVERT: A 3 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8773 (pp) REVERT: A 182 LEU cc_start: 0.9026 (mp) cc_final: 0.8817 (mp) REVERT: A 190 LYS cc_start: 0.8821 (ttpt) cc_final: 0.8573 (ttpt) outliers start: 6 outliers final: 4 residues processed: 50 average time/residue: 0.6482 time to fit residues: 32.9161 Evaluate side-chains 51 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 189 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 4 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 20 optimal weight: 0.1980 chunk 1 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 11 optimal weight: 0.0970 chunk 12 optimal weight: 0.2980 chunk 25 optimal weight: 0.4980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 134 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.121176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.108742 restraints weight = 2345.997| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 0.96 r_work: 0.3090 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.0859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2191 Z= 0.163 Angle : 0.487 7.192 2944 Z= 0.272 Chirality : 0.035 0.112 336 Planarity : 0.003 0.027 393 Dihedral : 4.647 40.211 305 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 2.14 % Allowed : 22.65 % Favored : 75.21 % 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: 3.44 (0.48), residues: 278 helix: 3.40 (0.33), residues: 204 sheet: None (None), residues: 0 loop : -1.21 (0.59), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 209 TYR 0.003 0.001 TYR A 102 PHE 0.019 0.002 PHE A 18 TRP 0.002 0.001 TRP A 150 HIS 0.004 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 2191) covalent geometry : angle 0.48709 ( 2944) hydrogen bonds : bond 0.07079 ( 179) hydrogen bonds : angle 3.42225 ( 519) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 556 Ramachandran restraints generated. 278 Oldfield, 0 Emsley, 278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.053 Fit side-chains REVERT: A 3 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8775 (pp) REVERT: A 182 LEU cc_start: 0.9040 (mp) cc_final: 0.8822 (mp) REVERT: A 190 LYS cc_start: 0.8817 (mtpt) cc_final: 0.8579 (ttpt) outliers start: 5 outliers final: 4 residues processed: 48 average time/residue: 0.5397 time to fit residues: 26.3254 Evaluate side-chains 52 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 189 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 2 optimal weight: 0.2980 chunk 24 optimal weight: 0.2980 chunk 5 optimal weight: 0.9980 chunk 22 optimal weight: 0.0970 chunk 4 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.121072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.108589 restraints weight = 2385.859| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 0.97 r_work: 0.3078 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.0810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2191 Z= 0.172 Angle : 0.499 8.024 2944 Z= 0.277 Chirality : 0.036 0.112 336 Planarity : 0.003 0.029 393 Dihedral : 4.717 41.131 305 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 2.56 % Allowed : 22.22 % Favored : 75.21 % 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: 3.37 (0.48), residues: 278 helix: 3.34 (0.33), residues: 204 sheet: None (None), residues: 0 loop : -1.21 (0.59), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 209 TYR 0.004 0.001 TYR A 102 PHE 0.020 0.002 PHE A 18 TRP 0.002 0.001 TRP A 150 HIS 0.005 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 2191) covalent geometry : angle 0.49915 ( 2944) hydrogen bonds : bond 0.07279 ( 179) hydrogen bonds : angle 3.46459 ( 519) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1226.94 seconds wall clock time: 21 minutes 33.61 seconds (1293.61 seconds total)